4-131331200-T-G

Variant names:

• chr4-131331200-T-G
• rs7676822

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 0.287 in 151,878 control chromosomes in the GnomAD database, including 6,440 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 0.29 (6440 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0810
• Publications: 3 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 (AMR) allele frequency at 95% confidence interval = 0.312 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.287 AC: 43622 AN: 151760 Hom.: 6434 Cov.: 32

Gnomad AFR AF: 0.237

Gnomad AMI AF: 0.254

Gnomad AMR AF: 0.319

Gnomad ASJ AF: 0.319

Gnomad EAS AF: 0.195

Gnomad SAS AF: 0.288

Gnomad FIN AF: 0.295

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.315

Gnomad OTH AF: 0.301

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

GnomAD4 genome AF: 0.287 AC: 43652 AN: 151878 Hom.: 6440 Cov.: 32 AF XY: 0.286 AC XY: 21223 AN XY: 74210

African (AFR) AF: 0.236 AC: 9808 AN: 41490

American (AMR) AF: 0.320 AC: 4873 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.319 AC: 1107 AN: 3468

East Asian (EAS) AF: 0.196 AC: 1009 AN: 5150

South Asian (SAS) AF: 0.289 AC: 1394 AN: 4820

European-Finnish (FIN) AF: 0.295 AC: 3119 AN: 10560

Middle Eastern (MID) AF: 0.340 AC: 100 AN: 294

European-Non Finnish (NFE) AF: 0.315 AC: 21376 AN: 67842

Other (OTH) AF: 0.302 AC: 636 AN: 2106

Alfa AF: 0.309 Hom.: 11258

Bravo AF: 0.288

Asia WGS AF: 0.280 AC: 972 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	3.0
DANN	Benign	0.59
PhyloP100		0.081

Splicing

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

Other links and lift over

dbSNP: rs7676822; hg19: chr4-132252355;