rs4626276

Variant names:

• chr4-110728833-A-C
• rs4626276

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 0.148 in 151,612 control chromosomes in the GnomAD database, including 2,015 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 0.15 (2015 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.495
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.342 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.148 AC: 22491 AN: 151494 Hom.: 2013 Cov.: 30

Gnomad AFR AF: 0.117

Gnomad AMI AF: 0.0504

Gnomad AMR AF: 0.203

Gnomad ASJ AF: 0.323

Gnomad EAS AF: 0.354

Gnomad SAS AF: 0.131

Gnomad FIN AF: 0.147

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.133

Gnomad OTH AF: 0.164

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

GnomAD4 genome AF: 0.148 AC: 22509 AN: 151612 Hom.: 2015 Cov.: 30 AF XY: 0.155 AC XY: 11472 AN XY: 74058

African (AFR) AF: 0.117 AC: 4820 AN: 41330

American (AMR) AF: 0.203 AC: 3093 AN: 15214

Ashkenazi Jewish (ASJ) AF: 0.323 AC: 1116 AN: 3460

East Asian (EAS) AF: 0.355 AC: 1813 AN: 5100

South Asian (SAS) AF: 0.131 AC: 626 AN: 4788

European-Finnish (FIN) AF: 0.147 AC: 1545 AN: 10516

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.133 AC: 9037 AN: 67894

Other (OTH) AF: 0.165 AC: 348 AN: 2104

Alfa AF: 0.136 Hom.: 1242

Bravo AF: 0.152

Asia WGS AF: 0.194 AC: 674 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.4
DANN	Benign	0.67
PhyloP100		0.49

Splicing

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

Other links and lift over

dbSNP: rs4626276; hg19: chr4-111649989;