rs10516624

Variant names:

• chr4-115863802-G-A
• rs10516624

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 0.245 in 151,162 control chromosomes in the GnomAD database, including 4,802 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 0.25 (4802 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0580
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.286 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: 0.245 AC: 37059 AN: 151040 Hom.: 4797 Cov.: 31

Gnomad AFR AF: 0.177

Gnomad AMI AF: 0.248

Gnomad AMR AF: 0.226

Gnomad ASJ AF: 0.375

Gnomad EAS AF: 0.216

Gnomad SAS AF: 0.263

Gnomad FIN AF: 0.217

Gnomad MID AF: 0.333

Gnomad NFE AF: 0.289

Gnomad OTH AF: 0.261

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

GnomAD4 genome AF: 0.245 AC: 37089 AN: 151162 Hom.: 4802 Cov.: 31 AF XY: 0.243 AC XY: 17958 AN XY: 73866

African (AFR) AF: 0.177 AC: 7324 AN: 41298

American (AMR) AF: 0.225 AC: 3407 AN: 15116

Ashkenazi Jewish (ASJ) AF: 0.375 AC: 1296 AN: 3458

East Asian (EAS) AF: 0.216 AC: 1111 AN: 5154

South Asian (SAS) AF: 0.265 AC: 1275 AN: 4818

European-Finnish (FIN) AF: 0.217 AC: 2289 AN: 10536

Middle Eastern (MID) AF: 0.333 AC: 96 AN: 288

European-Non Finnish (NFE) AF: 0.289 AC: 19519 AN: 67492

Other (OTH) AF: 0.261 AC: 547 AN: 2094

Alfa AF: 0.257 Hom.: 675

Bravo AF: 0.243

Asia WGS AF: 0.241 AC: 838 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.64
DANN	Benign	0.37
PhyloP100		-0.058

Splicing

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

Other links and lift over

dbSNP: rs10516624; hg19: chr4-116784958;