1-29959372-T-C

Variant names:

• chr1-29959372-T-C
• rs4949526

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 0.546 in 152,054 control chromosomes in the GnomAD database, including 26,412 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 0.55 (26412 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.433
• Publications: 18 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 (EAS) allele frequency at 95% confidence interval = 0.716 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.546 AC: 82994 AN: 151936 Hom.: 26409 Cov.: 32

Gnomad AFR AF: 0.195

Gnomad AMI AF: 0.660

Gnomad AMR AF: 0.587

Gnomad ASJ AF: 0.652

Gnomad EAS AF: 0.735

Gnomad SAS AF: 0.508

Gnomad FIN AF: 0.729

Gnomad MID AF: 0.586

Gnomad NFE AF: 0.702

Gnomad OTH AF: 0.586

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

GnomAD4 genome AF: 0.546 AC: 83018 AN: 152054 Hom.: 26412 Cov.: 32 AF XY: 0.547 AC XY: 40652 AN XY: 74302

African (AFR) AF: 0.195 AC: 8099 AN: 41474

American (AMR) AF: 0.587 AC: 8963 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.652 AC: 2265 AN: 3472

East Asian (EAS) AF: 0.736 AC: 3783 AN: 5142

South Asian (SAS) AF: 0.509 AC: 2451 AN: 4818

European-Finnish (FIN) AF: 0.729 AC: 7701 AN: 10568

Middle Eastern (MID) AF: 0.596 AC: 174 AN: 292

European-Non Finnish (NFE) AF: 0.702 AC: 47746 AN: 67996

Other (OTH) AF: 0.585 AC: 1234 AN: 2110

Alfa AF: 0.653 Hom.: 98327

Bravo AF: 0.524

Asia WGS AF: 0.540 AC: 1883 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.91
DANN	Benign	0.27
PhyloP100		-0.43

Splicing

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

Other links and lift over

dbSNP: rs4949526; hg19: chr1-30432219; COSMIC: COSV59934482;