rs10516630

Variant names:

• chr4-116403760-T-C
• rs10516630

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.0347 in 152,212 control chromosomes in the GnomAD database, including 227 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 0.035 (227 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.115

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0985 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: 0.0346 AC: 5270 AN: 152094 Hom.: 227 Cov.: 32

Gnomad AFR AF: 0.101

Gnomad AMI AF: 0.00987

Gnomad AMR AF: 0.0195

Gnomad ASJ AF: 0.0176

Gnomad EAS AF: 0.00212

Gnomad SAS AF: 0.0211

Gnomad FIN AF: 0.000377

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.00788

Gnomad OTH AF: 0.0249

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

GnomAD4 genome AF: 0.0347 AC: 5282 AN: 152212 Hom.: 227 Cov.: 32 AF XY: 0.0337 AC XY: 2507 AN XY: 74422

Gnomad4 AFR AF: 0.101

Gnomad4 AMR AF: 0.0194

Gnomad4 ASJ AF: 0.0176

Gnomad4 EAS AF: 0.00212

Gnomad4 SAS AF: 0.0210

Gnomad4 FIN AF: 0.000377

Gnomad4 NFE AF: 0.00788

Gnomad4 OTH AF: 0.0251

Alfa AF: 0.0252 Hom.: 19

Bravo AF: 0.0385

Asia WGS AF: 0.0160 AC: 57 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.94
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10516630; hg19: chr4-117324916;