chr4-117158751-G-A

Variant names:

• chr4-117158751-G-A
• rs10516635

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 0.136 in 152,078 control chromosomes in the GnomAD database, including 1,557 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 0.14 (1557 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.110
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.227 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: 0.136 AC: 20673 AN: 151960 Hom.: 1556 Cov.: 32

Gnomad AFR AF: 0.152

Gnomad AMI AF: 0.163

Gnomad AMR AF: 0.0918

Gnomad ASJ AF: 0.128

Gnomad EAS AF: 0.239

Gnomad SAS AF: 0.193

Gnomad FIN AF: 0.150

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.122

Gnomad OTH AF: 0.137

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

GnomAD4 genome AF: 0.136 AC: 20670 AN: 152078 Hom.: 1557 Cov.: 32 AF XY: 0.140 AC XY: 10406 AN XY: 74348

African (AFR) AF: 0.151 AC: 6289 AN: 41514

American (AMR) AF: 0.0918 AC: 1402 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.128 AC: 445 AN: 3468

East Asian (EAS) AF: 0.238 AC: 1233 AN: 5176

South Asian (SAS) AF: 0.193 AC: 932 AN: 4822

European-Finnish (FIN) AF: 0.150 AC: 1588 AN: 10584

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.122 AC: 8302 AN: 67922

Other (OTH) AF: 0.136 AC: 286 AN: 2110

Alfa AF: 0.124 Hom.: 4536

Bravo AF: 0.129

Asia WGS AF: 0.203 AC: 703 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.4
DANN	Benign	0.61
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs10516635; hg19: chr4-118079907;