rs10516563

chr4-110756566-T-G

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;