rs4691238

Variant names:

• chr4-156042540-G-A
• rs4691238

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 0.306 in 151,254 control chromosomes in the GnomAD database, including 8,969 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 0.31 (8969 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0160
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.411 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: 0.306 AC: 46293 AN: 151138 Hom.: 8967 Cov.: 32

Gnomad AFR AF: 0.110

Gnomad AMI AF: 0.444

Gnomad AMR AF: 0.355

Gnomad ASJ AF: 0.358

Gnomad EAS AF: 0.314

Gnomad SAS AF: 0.190

Gnomad FIN AF: 0.325

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.415

Gnomad OTH AF: 0.313

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

GnomAD4 genome AF: 0.306 AC: 46303 AN: 151254 Hom.: 8969 Cov.: 32 AF XY: 0.299 AC XY: 22085 AN XY: 73806

African (AFR) AF: 0.110 AC: 4558 AN: 41478

American (AMR) AF: 0.355 AC: 5357 AN: 15108

Ashkenazi Jewish (ASJ) AF: 0.358 AC: 1240 AN: 3466

East Asian (EAS) AF: 0.314 AC: 1619 AN: 5158

South Asian (SAS) AF: 0.192 AC: 895 AN: 4664

European-Finnish (FIN) AF: 0.325 AC: 3369 AN: 10382

Middle Eastern (MID) AF: 0.289 AC: 85 AN: 294

European-Non Finnish (NFE) AF: 0.415 AC: 28122 AN: 67700

Other (OTH) AF: 0.313 AC: 655 AN: 2096

Alfa AF: 0.376 Hom.: 21943

Bravo AF: 0.307

Asia WGS AF: 0.251 AC: 869 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	11
DANN	Benign	0.91
PhyloP100		0.016

Splicing

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

Other links and lift over

dbSNP: rs4691238; hg19: chr4-156963692;