20-3079704-A-C

Variant names:

• chr20-3079704-A-C
• rs1410713

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.622 in 152,044 control chromosomes in the GnomAD database, including 30,470 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 0.62 (30470 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.240
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.711 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.622 AC: 94565 AN: 151926 Hom.: 30451 Cov.: 32

Gnomad AFR AF: 0.442

Gnomad AMI AF: 0.474

Gnomad AMR AF: 0.718

Gnomad ASJ AF: 0.660

Gnomad EAS AF: 0.731

Gnomad SAS AF: 0.690

Gnomad FIN AF: 0.685

Gnomad MID AF: 0.599

Gnomad NFE AF: 0.688

Gnomad OTH AF: 0.616

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.622 AC: 94632 AN: 152044 Hom.: 30470 Cov.: 32 AF XY: 0.626 AC XY: 46489 AN XY: 74304

African (AFR) AF: 0.442 AC: 18317 AN: 41454

American (AMR) AF: 0.718 AC: 10970 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.660 AC: 2290 AN: 3470

East Asian (EAS) AF: 0.731 AC: 3780 AN: 5174

South Asian (SAS) AF: 0.690 AC: 3330 AN: 4824

European-Finnish (FIN) AF: 0.685 AC: 7236 AN: 10564

Middle Eastern (MID) AF: 0.603 AC: 176 AN: 292

European-Non Finnish (NFE) AF: 0.688 AC: 46798 AN: 67980

Other (OTH) AF: 0.620 AC: 1305 AN: 2106

Alfa AF: 0.669 Hom.: 7012

Bravo AF: 0.615

Asia WGS AF: 0.704 AC: 2442 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	6.8
DANN	Benign	0.93
PhyloP100		0.24

Splicing

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

Other links and lift over

dbSNP: rs1410713; hg19: chr20-3060350;