chr1-234534101-T-C

Variant names:

• chr1-234534101-T-C
• rs271762

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.494 in 152,052 control chromosomes in the GnomAD database, including 19,689 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 0.49 (19689 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 5.24
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.4).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.9 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: 0.494 AC: 75078 AN: 151934 Hom.: 19662 Cov.: 32

Gnomad AFR AF: 0.551

Gnomad AMI AF: 0.525

Gnomad AMR AF: 0.574

Gnomad ASJ AF: 0.458

Gnomad EAS AF: 0.922

Gnomad SAS AF: 0.776

Gnomad FIN AF: 0.428

Gnomad MID AF: 0.547

Gnomad NFE AF: 0.401

Gnomad OTH AF: 0.489

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

GnomAD4 genome AF: 0.494 AC: 75157 AN: 152052 Hom.: 19689 Cov.: 32 AF XY: 0.506 AC XY: 37643 AN XY: 74324

African (AFR) AF: 0.551 AC: 22848 AN: 41478

American (AMR) AF: 0.575 AC: 8779 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.458 AC: 1590 AN: 3470

East Asian (EAS) AF: 0.922 AC: 4760 AN: 5162

South Asian (SAS) AF: 0.775 AC: 3736 AN: 4818

European-Finnish (FIN) AF: 0.428 AC: 4522 AN: 10562

Middle Eastern (MID) AF: 0.548 AC: 161 AN: 294

European-Non Finnish (NFE) AF: 0.401 AC: 27238 AN: 67968

Other (OTH) AF: 0.495 AC: 1045 AN: 2112

Alfa AF: 0.430 Hom.: 19239

Bravo AF: 0.505

Asia WGS AF: 0.825 AC: 2864 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.40
CADD	Benign	17
DANN	Benign	0.86
PhyloP100		5.2

Splicing

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

Other links and lift over

dbSNP: rs271762; hg19: chr1-234669847;