chr20-3716971-T-C

Variant names:

• chr20-3716971-T-C
• rs4815597

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 0.777 in 151,750 control chromosomes in the GnomAD database, including 46,830 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 0.78 (46830 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.347
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.929 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.777 AC: 117777 AN: 151632 Hom.: 46778 Cov.: 30

Gnomad AFR AF: 0.936

Gnomad AMI AF: 0.432

Gnomad AMR AF: 0.759

Gnomad ASJ AF: 0.636

Gnomad EAS AF: 0.727

Gnomad SAS AF: 0.799

Gnomad FIN AF: 0.773

Gnomad MID AF: 0.687

Gnomad NFE AF: 0.700

Gnomad OTH AF: 0.741

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

GnomAD4 genome AF: 0.777 AC: 117886 AN: 151750 Hom.: 46830 Cov.: 30 AF XY: 0.781 AC XY: 57897 AN XY: 74138

African (AFR) AF: 0.936 AC: 38799 AN: 41430

American (AMR) AF: 0.759 AC: 11525 AN: 15186

Ashkenazi Jewish (ASJ) AF: 0.636 AC: 2201 AN: 3458

East Asian (EAS) AF: 0.727 AC: 3756 AN: 5168

South Asian (SAS) AF: 0.800 AC: 3835 AN: 4796

European-Finnish (FIN) AF: 0.773 AC: 8154 AN: 10550

Middle Eastern (MID) AF: 0.701 AC: 206 AN: 294

European-Non Finnish (NFE) AF: 0.700 AC: 47466 AN: 67852

Other (OTH) AF: 0.736 AC: 1551 AN: 2106

Alfa AF: 0.721 Hom.: 48636

Bravo AF: 0.779

Asia WGS AF: 0.732 AC: 2549 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	4.0
DANN	Benign	0.79
PhyloP100		-0.35

Splicing

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

Other links and lift over

dbSNP: rs4815597; hg19: chr20-3697618;