rs1614627

chr1-20620263-A-C

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.773

Gnomad4 AMR AF: 0.891

Gnomad4 ASJ AF: 0.934

Gnomad4 EAS AF: 0.683

Gnomad4 SAS AF: 0.725

Gnomad4 FIN AF: 0.889

Gnomad4 NFE AF: 0.922

Gnomad4 OTH AF: 0.881

Alfa AF: 0.912 Hom.: 80417

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1614627; hg19: chr1-20946756;