rs10516563

Variant names:

• chr4-110756566-T-G
• rs10516563

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 0.162 in 152,196 control chromosomes in the GnomAD database, including 2,371 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 0.16 (2371 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.136

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.387 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: 0.162 AC: 24613 AN: 152078 Hom.: 2368 Cov.: 32

Gnomad AFR AF: 0.168

Gnomad AMI AF: 0.0132

Gnomad AMR AF: 0.197

Gnomad ASJ AF: 0.308

Gnomad EAS AF: 0.400

Gnomad SAS AF: 0.118

Gnomad FIN AF: 0.151

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.131

Gnomad OTH AF: 0.168

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

GnomAD4 genome AF: 0.162 AC: 24643 AN: 152196 Hom.: 2371 Cov.: 32 AF XY: 0.168 AC XY: 12520 AN XY: 74414

Gnomad4 AFR AF: 0.168

Gnomad4 AMR AF: 0.197

Gnomad4 ASJ AF: 0.308

Gnomad4 EAS AF: 0.401

Gnomad4 SAS AF: 0.118

Gnomad4 FIN AF: 0.151

Gnomad4 NFE AF: 0.131

Gnomad4 OTH AF: 0.168

Alfa AF: 0.141 Hom.: 1740

Bravo AF: 0.166

Asia WGS AF: 0.199 AC: 693 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.9
DANN	Benign	0.86

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10516563; hg19: chr4-111677722;