rs4653109

Variant names:

• chr1-34862644-A-G
• rs4653109

Your query was ambiguous. Multiple possible variants found:

• chr1-34862644-A-G
• chr1-34862644-A-T

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 0.412 in 152,076 control chromosomes in the GnomAD database, including 13,935 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 0.41 (13935 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.395
• Publications: 12 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.938 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: 0.412 AC: 62565 AN: 151958 Hom.: 13897 Cov.: 32

Gnomad AFR AF: 0.387

Gnomad AMI AF: 0.227

Gnomad AMR AF: 0.500

Gnomad ASJ AF: 0.400

Gnomad EAS AF: 0.960

Gnomad SAS AF: 0.578

Gnomad FIN AF: 0.406

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.358

Gnomad OTH AF: 0.414

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

GnomAD4 genome AF: 0.412 AC: 62665 AN: 152076 Hom.: 13935 Cov.: 32 AF XY: 0.424 AC XY: 31525 AN XY: 74334

African (AFR) AF: 0.388 AC: 16084 AN: 41480

American (AMR) AF: 0.500 AC: 7646 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.400 AC: 1389 AN: 3472

East Asian (EAS) AF: 0.960 AC: 4963 AN: 5170

South Asian (SAS) AF: 0.578 AC: 2787 AN: 4818

European-Finnish (FIN) AF: 0.406 AC: 4291 AN: 10560

Middle Eastern (MID) AF: 0.327 AC: 96 AN: 294

European-Non Finnish (NFE) AF: 0.358 AC: 24311 AN: 67970

Other (OTH) AF: 0.421 AC: 891 AN: 2114

Alfa AF: 0.385 Hom.: 28420

Bravo AF: 0.414

Asia WGS AF: 0.748 AC: 2598 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	7.0
DANN	Benign	0.66
PhyloP100		0.40

Splicing

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

Other links and lift over

dbSNP: rs4653109; hg19: chr1-35328245;