rs10516623

Variant names:

• chr4-115863716-A-C
• rs10516623

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 0.259 in 151,212 control chromosomes in the GnomAD database, including 5,221 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 0.26 (5221 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• 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: 0.259 AC: 39120 AN: 151094 Hom.: 5211 Cov.: 30

Gnomad AFR AF: 0.225

Gnomad AMI AF: 0.248

Gnomad AMR AF: 0.229

Gnomad ASJ AF: 0.374

Gnomad EAS AF: 0.215

Gnomad SAS AF: 0.263

Gnomad FIN AF: 0.217

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.290

Gnomad OTH AF: 0.268

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

GnomAD4 genome AF: 0.259 AC: 39168 AN: 151212 Hom.: 5221 Cov.: 30 AF XY: 0.256 AC XY: 18878 AN XY: 73862

African (AFR) AF: 0.226 AC: 9337 AN: 41366

American (AMR) AF: 0.229 AC: 3452 AN: 15104

Ashkenazi Jewish (ASJ) AF: 0.374 AC: 1292 AN: 3452

East Asian (EAS) AF: 0.215 AC: 1105 AN: 5144

South Asian (SAS) AF: 0.265 AC: 1275 AN: 4810

European-Finnish (FIN) AF: 0.217 AC: 2279 AN: 10524

Middle Eastern (MID) AF: 0.330 AC: 93 AN: 282

European-Non Finnish (NFE) AF: 0.289 AC: 19546 AN: 67522

Other (OTH) AF: 0.269 AC: 564 AN: 2100

Alfa AF: 0.265 Hom.: 714

Bravo AF: 0.258

Asia WGS AF: 0.245 AC: 850 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.4
DANN	Benign	0.19
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs10516623; hg19: chr4-116784872;