dbSNP rs1661281: ANKRD22:c.*2368C>T (chr10-88820573-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_144590.3(ANKRD22):c.*2368C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.305 in 1,410,004 control chromosomes in the GnomAD database, including 66,517 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.26 ( 5776 hom., cov: 32)

Exomes 𝑓: 0.31 ( 60741 hom. )

Consequence

ANKRD22
NM_144590.3 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.119

Publications

10 publications found

Variant links:

COSMIC-nc: COSV64237187

Genes affected

ANKRD22 (HGNC:28321): (ankyrin repeat domain 22)

ANKRD22 links:

LIPM (HGNC:23455): (lipase family member M) Predicted to enable lipoprotein lipase activity. Predicted to be involved in cornification. Predicted to be located in extracellular region. [provided by Alliance of Genome Resources, Apr 2022]

LIPM links:

Genome browser will be placed here

new If you want to explore the variant's impact on the transcript NM_144590.3, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.86).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.357 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_144590.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ANKRD22	NM_144590.3	MANE Select	c.*2368C>T		3_prime_UTR	Exon 6 of 6	NP_653191.2	Q5VYY1
	LIPM	NM_001128215.1	MANE Select	c.*72G>A		downstream_gene	N/A	NP_001121687.1	Q5VYY2-1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
ANKRD22	ENST00000371930.5	TSL:1 MANE Select	c.*2368C>T	3_prime_UTR	Exon 6 of 6	ENSP00000360998.4	Q5VYY1
LIPM	ENST00000404743.9	TSL:1 MANE Select	c.*72G>A	downstream_gene	N/A	ENSP00000383901.3	Q5VYY2-1
LIPM	ENST00000539337.2	TSL:2	c.*72G>A	downstream_gene	N/A	ENSP00000440375.1	Q5VYY2-2

Frequencies

GnomAD3 genomes

AF:

0.261

AC:

39727

AN:

151958

Hom.:

5775

Cov.:

show subpopulations

Gnomad AFR

AF:

0.122

Gnomad AMI

AF:

0.319

Gnomad AMR

AF:

0.318

Gnomad ASJ

AF:

0.306

Gnomad EAS

AF:

0.371

Gnomad SAS

AF:

0.333

Gnomad FIN

AF:

0.331

Gnomad MID

AF:

0.177

Gnomad NFE

AF:

0.306

Gnomad OTH

AF:

0.271

GnomAD4 exome

AF:

0.310

AC:

390165

AN:

1257928

Hom.:

60741

Cov.:

AF XY:

0.310

AC XY:

191330

AN XY:

616742

show subpopulations

African (AFR)

AF:

0.117

AC:

3335

AN:

28410

American (AMR)

AF:

0.341

AC:

9435

AN:

27638

Ashkenazi Jewish (ASJ)

AF:

0.309

AC:

6367

AN:

20632

East Asian (EAS)

AF:

0.394

AC:

13705

AN:

34818

South Asian (SAS)

AF:

0.323

AC:

21703

AN:

67100

European-Finnish (FIN)

AF:

0.326

AC:

11798

AN:

36186

Middle Eastern (MID)

AF:

0.248

AC:

912

AN:

3676

European-Non Finnish (NFE)

AF:

0.311

AC:

307290

AN:

986730

Other (OTH)

AF:

0.296

AC:

15620

AN:

52738

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.510

Heterozygous variant carriers

13457

26914

40372

53829

67286

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

10358

20716

31074

41432

51790

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.261

AC:

39730

AN:

152076

Hom.:

5776

Cov.:

AF XY:

0.266

AC XY:

19777

AN XY:

74324

show subpopulations

African (AFR)

AF:

0.122

AC:

5056

AN:

41504

American (AMR)

AF:

0.318

AC:

4864

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.306

AC:

1063

AN:

3472

East Asian (EAS)

AF:

0.371

AC:

1917

AN:

5170

South Asian (SAS)

AF:

0.333

AC:

1607

AN:

4820

European-Finnish (FIN)

AF:

0.331

AC:

3483

AN:

10536

Middle Eastern (MID)

AF:

0.184

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.306

AC:

20819

AN:

67962

Other (OTH)

AF:

0.272

AC:

576

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1460

2920

4379

5839

7299

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

422

844

1266

1688

2110

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.290

Hom.:

20078

Bravo

AF:

0.255

Asia WGS

AF:

0.313

AC:

1088

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

1.6

(source)

DANN

Benign

0.68

PhyloP100

-0.12

Mutation Taster

=100/0

polymorphism

(source)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over