1-40609537-C-T

Variant names:

• chr1-40609537-C-T
• rs500586

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 0.68 in 151,992 control chromosomes in the GnomAD database, including 35,457 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 0.68 (35457 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.745
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.755 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: 0.680 AC: 103293 AN: 151874 Hom.: 35450 Cov.: 31

Gnomad AFR AF: 0.763

Gnomad AMI AF: 0.656

Gnomad AMR AF: 0.593

Gnomad ASJ AF: 0.648

Gnomad EAS AF: 0.523

Gnomad SAS AF: 0.523

Gnomad FIN AF: 0.636

Gnomad MID AF: 0.756

Gnomad NFE AF: 0.681

Gnomad OTH AF: 0.679

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

GnomAD4 genome AF: 0.680 AC: 103349 AN: 151992 Hom.: 35457 Cov.: 31 AF XY: 0.674 AC XY: 50081 AN XY: 74270

African (AFR) AF: 0.762 AC: 31627 AN: 41482

American (AMR) AF: 0.592 AC: 9028 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.648 AC: 2247 AN: 3470

East Asian (EAS) AF: 0.523 AC: 2692 AN: 5150

South Asian (SAS) AF: 0.525 AC: 2525 AN: 4814

European-Finnish (FIN) AF: 0.636 AC: 6715 AN: 10560

Middle Eastern (MID) AF: 0.752 AC: 221 AN: 294

European-Non Finnish (NFE) AF: 0.681 AC: 46280 AN: 67956

Other (OTH) AF: 0.673 AC: 1416 AN: 2104

Alfa AF: 0.678 Hom.: 57663

Bravo AF: 0.681

Asia WGS AF: 0.541 AC: 1881 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.23
PhyloP100		-0.74

Splicing

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

Other links and lift over

dbSNP: rs500586; hg19: chr1-41075209;