rs6662618

Variant names:

• chr1-92469854-T-G
• rs6662618

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 0.758 in 152,074 control chromosomes in the GnomAD database, including 45,011 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 0.76 (45011 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.290
• Publications: 24 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.95 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: 0.759 AC: 115304 AN: 151956 Hom.: 45007 Cov.: 33

Gnomad AFR AF: 0.569

Gnomad AMI AF: 0.945

Gnomad AMR AF: 0.744

Gnomad ASJ AF: 0.753

Gnomad EAS AF: 0.972

Gnomad SAS AF: 0.856

Gnomad FIN AF: 0.859

Gnomad MID AF: 0.804

Gnomad NFE AF: 0.837

Gnomad OTH AF: 0.744

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

GnomAD4 genome AF: 0.758 AC: 115336 AN: 152074 Hom.: 45011 Cov.: 33 AF XY: 0.760 AC XY: 56480 AN XY: 74360

African (AFR) AF: 0.568 AC: 23521 AN: 41408

American (AMR) AF: 0.744 AC: 11370 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.753 AC: 2616 AN: 3472

East Asian (EAS) AF: 0.973 AC: 5044 AN: 5186

South Asian (SAS) AF: 0.855 AC: 4133 AN: 4832

European-Finnish (FIN) AF: 0.859 AC: 9085 AN: 10576

Middle Eastern (MID) AF: 0.799 AC: 235 AN: 294

European-Non Finnish (NFE) AF: 0.837 AC: 56894 AN: 67992

Other (OTH) AF: 0.747 AC: 1576 AN: 2110

Alfa AF: 0.811 Hom.: 98039

Bravo AF: 0.743

Asia WGS AF: 0.884 AC: 3066 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	3.6
DANN	Benign	0.67
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs6662618; hg19: chr1-92935411;