chr1-29926467-T-C

Variant names:

• chr1-29926467-T-C
• rs174837

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 0.799 in 152,062 control chromosomes in the GnomAD database, including 49,089 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 0.80 (49089 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.47
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.852 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: 0.800 AC: 121482 AN: 151946 Hom.: 49058 Cov.: 31

Gnomad AFR AF: 0.708

Gnomad AMI AF: 0.820

Gnomad AMR AF: 0.798

Gnomad ASJ AF: 0.841

Gnomad EAS AF: 0.722

Gnomad SAS AF: 0.683

Gnomad FIN AF: 0.852

Gnomad MID AF: 0.839

Gnomad NFE AF: 0.858

Gnomad OTH AF: 0.829

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

GnomAD4 genome AF: 0.799 AC: 121560 AN: 152062 Hom.: 49089 Cov.: 31 AF XY: 0.798 AC XY: 59323 AN XY: 74328

African (AFR) AF: 0.708 AC: 29362 AN: 41460

American (AMR) AF: 0.797 AC: 12186 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.841 AC: 2918 AN: 3470

East Asian (EAS) AF: 0.721 AC: 3713 AN: 5148

South Asian (SAS) AF: 0.683 AC: 3290 AN: 4820

European-Finnish (FIN) AF: 0.852 AC: 9025 AN: 10590

Middle Eastern (MID) AF: 0.839 AC: 245 AN: 292

European-Non Finnish (NFE) AF: 0.858 AC: 58325 AN: 67972

Other (OTH) AF: 0.829 AC: 1748 AN: 2108

Alfa AF: 0.797 Hom.: 3333

Bravo AF: 0.794

Asia WGS AF: 0.718 AC: 2498 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.14
DANN	Benign	0.56
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs174837; hg19: chr1-30399314;