1-34862431-C-T

Variant names:

• chr1-34862431-C-T
• rs4653108

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 0.201 in 152,192 control chromosomes in the GnomAD database, including 4,955 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 0.20 (4955 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.169
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.62).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.802 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: 0.201 AC: 30547 AN: 152074 Hom.: 4948 Cov.: 33

Gnomad AFR AF: 0.0523

Gnomad AMI AF: 0.125

Gnomad AMR AF: 0.364

Gnomad ASJ AF: 0.229

Gnomad EAS AF: 0.823

Gnomad SAS AF: 0.367

Gnomad FIN AF: 0.279

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.183

Gnomad OTH AF: 0.212

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

GnomAD4 genome AF: 0.201 AC: 30563 AN: 152192 Hom.: 4955 Cov.: 33 AF XY: 0.218 AC XY: 16209 AN XY: 74412

African (AFR) AF: 0.0521 AC: 2163 AN: 41546

American (AMR) AF: 0.364 AC: 5568 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.229 AC: 794 AN: 3472

East Asian (EAS) AF: 0.823 AC: 4255 AN: 5172

South Asian (SAS) AF: 0.367 AC: 1772 AN: 4822

European-Finnish (FIN) AF: 0.279 AC: 2951 AN: 10584

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.183 AC: 12442 AN: 67988

Other (OTH) AF: 0.218 AC: 461 AN: 2114

Alfa AF: 0.186 Hom.: 6221

Bravo AF: 0.199

Asia WGS AF: 0.522 AC: 1814 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.62
CADD	Benign	14
DANN	Benign	0.81
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs4653108; hg19: chr1-35328032;