1-152640434-T-C

Variant names:

• chr1-152640434-T-C
• rs1325508

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 0.193 in 152,162 control chromosomes in the GnomAD database, including 4,269 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 0.19 (4269 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.103
• Publications: 11 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 = 0.391 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.193 AC: 29365 AN: 152044 Hom.: 4247 Cov.: 32

Gnomad AFR AF: 0.396

Gnomad AMI AF: 0.0121

Gnomad AMR AF: 0.160

Gnomad ASJ AF: 0.118

Gnomad EAS AF: 0.292

Gnomad SAS AF: 0.150

Gnomad FIN AF: 0.160

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.0847

Gnomad OTH AF: 0.180

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

GnomAD4 genome AF: 0.193 AC: 29422 AN: 152162 Hom.: 4269 Cov.: 32 AF XY: 0.196 AC XY: 14571 AN XY: 74390

African (AFR) AF: 0.396 AC: 16438 AN: 41462

American (AMR) AF: 0.160 AC: 2441 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.118 AC: 408 AN: 3470

East Asian (EAS) AF: 0.291 AC: 1507 AN: 5172

South Asian (SAS) AF: 0.149 AC: 718 AN: 4824

European-Finnish (FIN) AF: 0.160 AC: 1692 AN: 10594

Middle Eastern (MID) AF: 0.187 AC: 55 AN: 294

European-Non Finnish (NFE) AF: 0.0847 AC: 5762 AN: 68020

Other (OTH) AF: 0.185 AC: 390 AN: 2112

Alfa AF: 0.112 Hom.: 6378

Bravo AF: 0.202

Asia WGS AF: 0.257 AC: 894 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	5.5
DANN	Benign	0.74
PhyloP100		0.10

Splicing

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

Other links and lift over

dbSNP: rs1325508; hg19: chr1-152612910;