rs2347044

Variant names:

• chr4-43430905-T-C
• rs2347044

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 0.598 in 151,422 control chromosomes in the GnomAD database, including 32,687 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 0.60 (32687 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.36
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.818 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: 0.599 AC: 90627 AN: 151304 Hom.: 32698 Cov.: 31

Gnomad AFR AF: 0.216

Gnomad AMI AF: 0.921

Gnomad AMR AF: 0.602

Gnomad ASJ AF: 0.741

Gnomad EAS AF: 0.195

Gnomad SAS AF: 0.598

Gnomad FIN AF: 0.765

Gnomad MID AF: 0.693

Gnomad NFE AF: 0.824

Gnomad OTH AF: 0.628

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

GnomAD4 genome AF: 0.598 AC: 90621 AN: 151422 Hom.: 32687 Cov.: 31 AF XY: 0.591 AC XY: 43688 AN XY: 73952

African (AFR) AF: 0.216 AC: 8947 AN: 41428

American (AMR) AF: 0.602 AC: 9114 AN: 15150

Ashkenazi Jewish (ASJ) AF: 0.741 AC: 2563 AN: 3460

East Asian (EAS) AF: 0.195 AC: 1000 AN: 5126

South Asian (SAS) AF: 0.600 AC: 2883 AN: 4806

European-Finnish (FIN) AF: 0.765 AC: 8061 AN: 10540

Middle Eastern (MID) AF: 0.704 AC: 207 AN: 294

European-Non Finnish (NFE) AF: 0.824 AC: 55706 AN: 67610

Other (OTH) AF: 0.620 AC: 1300 AN: 2096

Alfa AF: 0.763 Hom.: 163555

Bravo AF: 0.570

Asia WGS AF: 0.353 AC: 1227 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	8.8
DANN	Benign	0.79
PhyloP100		1.4

Splicing

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

Other links and lift over

dbSNP: rs2347044; hg19: chr4-43432922;