rs1625

Variant names:

• chr20-11888961-T-A
• rs1625

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 0.333 in 152,070 control chromosomes in the GnomAD database, including 8,581 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 0.33 (8581 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.396
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.369 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: 0.333 AC: 50667 AN: 151952 Hom.: 8570 Cov.: 32

Gnomad AFR AF: 0.282

Gnomad AMI AF: 0.444

Gnomad AMR AF: 0.323

Gnomad ASJ AF: 0.291

Gnomad EAS AF: 0.221

Gnomad SAS AF: 0.269

Gnomad FIN AF: 0.390

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.372

Gnomad OTH AF: 0.321

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

GnomAD4 genome AF: 0.333 AC: 50701 AN: 152070 Hom.: 8581 Cov.: 32 AF XY: 0.334 AC XY: 24808 AN XY: 74336

African (AFR) AF: 0.282 AC: 11708 AN: 41484

American (AMR) AF: 0.322 AC: 4922 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.291 AC: 1010 AN: 3466

East Asian (EAS) AF: 0.221 AC: 1145 AN: 5174

South Asian (SAS) AF: 0.268 AC: 1293 AN: 4818

European-Finnish (FIN) AF: 0.390 AC: 4118 AN: 10550

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.372 AC: 25327 AN: 67994

Other (OTH) AF: 0.323 AC: 681 AN: 2108

Alfa AF: 0.353 Hom.: 1288

Bravo AF: 0.326

Asia WGS AF: 0.245 AC: 853 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.4
DANN	Benign	0.69
PhyloP100		-0.40

Splicing

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

Other links and lift over

dbSNP: rs1625; hg19: chr20-11869609;