rs1614627

Variant names:

• chr1-20620263-A-C
• rs1614627

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 0.862 in 152,062 control chromosomes in the GnomAD database, including 56,934 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 0.86 (56934 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.604
• Publications: 12 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 (NFE) allele frequency at 95% confidence interval = 0.916 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: 0.862 AC: 130926 AN: 151944 Hom.: 56897 Cov.: 30

Gnomad AFR AF: 0.773

Gnomad AMI AF: 0.962

Gnomad AMR AF: 0.891

Gnomad ASJ AF: 0.934

Gnomad EAS AF: 0.682

Gnomad SAS AF: 0.723

Gnomad FIN AF: 0.889

Gnomad MID AF: 0.949

Gnomad NFE AF: 0.922

Gnomad OTH AF: 0.888

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

GnomAD4 genome AF: 0.862 AC: 131013 AN: 152062 Hom.: 56934 Cov.: 30 AF XY: 0.858 AC XY: 63777 AN XY: 74314

African (AFR) AF: 0.773 AC: 32059 AN: 41488

American (AMR) AF: 0.891 AC: 13611 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.934 AC: 3240 AN: 3470

East Asian (EAS) AF: 0.683 AC: 3502 AN: 5128

South Asian (SAS) AF: 0.725 AC: 3482 AN: 4806

European-Finnish (FIN) AF: 0.889 AC: 9412 AN: 10592

Middle Eastern (MID) AF: 0.946 AC: 278 AN: 294

European-Non Finnish (NFE) AF: 0.922 AC: 62693 AN: 67984

Other (OTH) AF: 0.881 AC: 1859 AN: 2110

Alfa AF: 0.911 Hom.: 103972

Bravo AF: 0.860

Asia WGS AF: 0.716 AC: 2492 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	2.3
DANN	Benign	0.33
PhyloP100		-0.60

Splicing

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

Other links and lift over

dbSNP: rs1614627; hg19: chr1-20946756;