4-10186702-G-A

Variant names:

• chr4-10186702-G-A
• rs956312

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 0.601 in 152,034 control chromosomes in the GnomAD database, including 28,330 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 (28330 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.185
• Publications: 9 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 = 0.678 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: 0.601 AC: 91243 AN: 151916 Hom.: 28309 Cov.: 32

Gnomad AFR AF: 0.441

Gnomad AMI AF: 0.577

Gnomad AMR AF: 0.603

Gnomad ASJ AF: 0.585

Gnomad EAS AF: 0.540

Gnomad SAS AF: 0.678

Gnomad FIN AF: 0.695

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.683

Gnomad OTH AF: 0.602

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

GnomAD4 genome AF: 0.601 AC: 91301 AN: 152034 Hom.: 28330 Cov.: 32 AF XY: 0.602 AC XY: 44727 AN XY: 74296

African (AFR) AF: 0.441 AC: 18268 AN: 41458

American (AMR) AF: 0.604 AC: 9217 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.585 AC: 2031 AN: 3470

East Asian (EAS) AF: 0.540 AC: 2783 AN: 5154

South Asian (SAS) AF: 0.678 AC: 3264 AN: 4812

European-Finnish (FIN) AF: 0.695 AC: 7349 AN: 10576

Middle Eastern (MID) AF: 0.507 AC: 149 AN: 294

European-Non Finnish (NFE) AF: 0.683 AC: 46456 AN: 67976

Other (OTH) AF: 0.596 AC: 1258 AN: 2110

Alfa AF: 0.650 Hom.: 102924

Bravo AF: 0.582

Asia WGS AF: 0.619 AC: 2152 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.47
DANN	Benign	0.22
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs956312; hg19: chr4-10188326;