1-153067689-C-T

Variant names:

• chr1-153067689-C-T
• rs576941

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 0.566 in 151,906 control chromosomes in the GnomAD database, including 25,156 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 0.57 (25156 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.972
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.711 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: 0.566 AC: 85930 AN: 151788 Hom.: 25117 Cov.: 32

Gnomad AFR AF: 0.718

Gnomad AMI AF: 0.375

Gnomad AMR AF: 0.492

Gnomad ASJ AF: 0.520

Gnomad EAS AF: 0.663

Gnomad SAS AF: 0.522

Gnomad FIN AF: 0.464

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.508

Gnomad OTH AF: 0.546

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

GnomAD4 genome AF: 0.566 AC: 86026 AN: 151906 Hom.: 25156 Cov.: 32 AF XY: 0.562 AC XY: 41720 AN XY: 74254

African (AFR) AF: 0.718 AC: 29763 AN: 41436

American (AMR) AF: 0.492 AC: 7512 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.520 AC: 1803 AN: 3468

East Asian (EAS) AF: 0.663 AC: 3426 AN: 5170

South Asian (SAS) AF: 0.522 AC: 2512 AN: 4816

European-Finnish (FIN) AF: 0.464 AC: 4892 AN: 10544

Middle Eastern (MID) AF: 0.527 AC: 155 AN: 294

European-Non Finnish (NFE) AF: 0.508 AC: 34474 AN: 67900

Other (OTH) AF: 0.545 AC: 1148 AN: 2106

Alfa AF: 0.525 Hom.: 3685

Bravo AF: 0.577

Asia WGS AF: 0.568 AC: 1977 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	0.96
DANN	Benign	0.34
PhyloP100		-0.97

Splicing

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

Other links and lift over

dbSNP: rs576941; hg19: chr1-153040165;