dbSNP rs56270809: ENSG00000291280:n.506T>G (chr21-13979932-A-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000766859.1(ENSG00000291280):n.253T>G variant causes a splice region, non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.266 in 1,245,642 control chromosomes in the GnomAD database, including 46,301 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 0.24 ( 4759 hom., cov: 30)

Exomes 𝑓: 0.27 ( 41542 hom. )

Consequence

ENSG00000291280
ENST00000766859.1 splice_region, non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.05

Publications

8 publications found

Variant links:

COSMIC-nc: COSV60948517

Genes affected

ENSG00000291280 (HGNC:):

ENSG00000291280 links:

ANKRD20A11P (HGNC:42024): (ankyrin repeat domain 20 family member A11, pseudogene)

ANKRD20A11P links:

Genome browser will be placed here

new If you want to explore the variant's impact on the transcript ENST00000766859.1, 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=-0.9).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.324 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000766859.1. 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
	ANKRD20A11P	NR_027270.1		n.513T>G		non_coding_transcript_exon	Exon 1 of 6

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank
ENSG00000291280	ENST00000344693.6	TSL:1	n.506T>G	non_coding_transcript_exon	Exon 1 of 8
ENSG00000291280	ENST00000428576.6	TSL:3	n.217T>G	non_coding_transcript_exon	Exon 1 of 9
ENSG00000291280	ENST00000766858.1		n.705T>G	non_coding_transcript_exon	Exon 1 of 8

Frequencies

GnomAD3 genomes

AF:

0.242

AC:

36648

AN:

151720

Hom.:

4743

Cov.:

show subpopulations

Gnomad AFR

AF:

0.166

Gnomad AMI

AF:

0.290

Gnomad AMR

AF:

0.324

Gnomad ASJ

AF:

0.314

Gnomad EAS

AF:

0.0921

Gnomad SAS

AF:

0.337

Gnomad FIN

AF:

0.212

Gnomad MID

AF:

0.296

Gnomad NFE

AF:

0.273

Gnomad OTH

AF:

0.257

GnomAD4 exome

AF:

0.269

AC:

294367

AN:

1093802

Hom.:

41542

Cov.:

AF XY:

0.272

AC XY:

151179

AN XY:

555816

show subpopulations

African (AFR)

AF:

0.163

AC:

4302

AN:

26456

American (AMR)

AF:

0.344

AC:

13045

AN:

37884

Ashkenazi Jewish (ASJ)

AF:

0.316

AC:

7013

AN:

22212

East Asian (EAS)

AF:

0.0876

AC:

3253

AN:

37126

South Asian (SAS)

AF:

0.339

AC:

25370

AN:

74898

European-Finnish (FIN)

AF:

0.218

AC:

10629

AN:

48690

Middle Eastern (MID)

AF:

0.293

AC:

988

AN:

3376

European-Non Finnish (NFE)

AF:

0.273

AC:

217165

AN:

795352

Other (OTH)

AF:

0.264

AC:

12602

AN:

47808

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.510

Heterozygous variant carriers

10290

20581

30871

41162

51452

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

6386

12772

19158

25544

31930

<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:

0.242

AC:

36707

AN:

151840

Hom.:

4759

Cov.:

AF XY:

0.240

AC XY:

17850

AN XY:

74230

show subpopulations

African (AFR)

AF:

0.166

AC:

6892

AN:

41406

American (AMR)

AF:

0.324

AC:

4955

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.314

AC:

1089

AN:

3464

East Asian (EAS)

AF:

0.0923

AC:

474

AN:

5136

South Asian (SAS)

AF:

0.337

AC:

1622

AN:

4808

European-Finnish (FIN)

AF:

0.212

AC:

2238

AN:

10552

Middle Eastern (MID)

AF:

0.282

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.273

AC:

18534

AN:

67890

Other (OTH)

AF:

0.264

AC:

556

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1389

2778

4168

5557

6946

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

382

764

1146

1528

1910

<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:

0.261

Hom.:

1747

Bravo

AF:

0.242

Asia WGS

AF:

0.225

AC:

779

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

3.9

(source)

DANN

Benign

0.30

PhyloP100

-1.0

Mutation Taster

=100/0

polymorphism (auto)

(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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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