chr4-186561531-T-G

Variant names:

• chr4-186561531-T-G
• rs7665392

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 0.104 in 152,102 control chromosomes in the GnomAD database, including 1,368 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 0.10 (1368 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.293
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.218 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: 0.104 AC: 15739 AN: 151984 Hom.: 1359 Cov.: 32

Gnomad AFR AF: 0.208

Gnomad AMI AF: 0.0230

Gnomad AMR AF: 0.138

Gnomad ASJ AF: 0.100

Gnomad EAS AF: 0.229

Gnomad SAS AF: 0.0993

Gnomad FIN AF: 0.0103

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0395

Gnomad OTH AF: 0.0986

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

GnomAD4 genome AF: 0.104 AC: 15787 AN: 152102 Hom.: 1368 Cov.: 32 AF XY: 0.104 AC XY: 7737 AN XY: 74348

African (AFR) AF: 0.208 AC: 8628 AN: 41452

American (AMR) AF: 0.138 AC: 2103 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.100 AC: 348 AN: 3470

East Asian (EAS) AF: 0.229 AC: 1184 AN: 5168

South Asian (SAS) AF: 0.0991 AC: 477 AN: 4812

European-Finnish (FIN) AF: 0.0103 AC: 109 AN: 10604

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.0395 AC: 2685 AN: 68002

Other (OTH) AF: 0.0994 AC: 210 AN: 2112

Alfa AF: 0.0979 Hom.: 204

Bravo AF: 0.118

Asia WGS AF: 0.156 AC: 546 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.9
DANN	Benign	0.56
PhyloP100		0.29

Splicing

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

Other links and lift over

dbSNP: rs7665392; hg19: chr4-187482685;