rs1408956

Variant names:

• chr1-67671380-C-T
• rs1408956

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 0.406 in 151,954 control chromosomes in the GnomAD database, including 14,730 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 0.41 (14730 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.24
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.521 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.406 AC: 61690 AN: 151836 Hom.: 14728 Cov.: 31

Gnomad AFR AF: 0.138

Gnomad AMI AF: 0.718

Gnomad AMR AF: 0.489

Gnomad ASJ AF: 0.494

Gnomad EAS AF: 0.372

Gnomad SAS AF: 0.526

Gnomad FIN AF: 0.467

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.526

Gnomad OTH AF: 0.445

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

GnomAD4 genome AF: 0.406 AC: 61688 AN: 151954 Hom.: 14730 Cov.: 31 AF XY: 0.404 AC XY: 29995 AN XY: 74286

African (AFR) AF: 0.138 AC: 5699 AN: 41428

American (AMR) AF: 0.490 AC: 7482 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.494 AC: 1713 AN: 3470

East Asian (EAS) AF: 0.371 AC: 1917 AN: 5162

South Asian (SAS) AF: 0.526 AC: 2533 AN: 4816

European-Finnish (FIN) AF: 0.467 AC: 4929 AN: 10564

Middle Eastern (MID) AF: 0.390 AC: 114 AN: 292

European-Non Finnish (NFE) AF: 0.526 AC: 35712 AN: 67934

Other (OTH) AF: 0.443 AC: 934 AN: 2106

Alfa AF: 0.452 Hom.: 3020

Bravo AF: 0.395

Asia WGS AF: 0.415 AC: 1444 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.95
DANN	Benign	0.25
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs1408956; hg19: chr1-68137063;