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

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ANKRD22	NM_144590.3 link	c.*2368C>T		3_prime_UTR_variant	Exon 6 of 6	ENST00000371930.5	NP_653191.2	Q5VYY1
LIPM	NM_001128215.1 link	c.*72G>A		downstream_gene_variant		ENST00000404743.9	NP_001121687.1	Q5VYY2-1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
ANKRD22	ENST00000371930.5 link	c.*2368C>T	3_prime_UTR_variant	Exon 6 of 6	1	NM_144590.3	ENSP00000360998.4	Q5VYY1
LIPM	ENST00000404743.9 link	c.*72G>A	downstream_gene_variant		1	NM_001128215.1	ENSP00000383901.3	Q5VYY2-1
LIPM	ENST00000539337.2 link	c.*72G>A	downstream_gene_variant		2		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

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

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 v4.3

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

Publications

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rs1661281

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over