rs10516747

chr4-85444959-A-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 0.0174 in 152,358 control chromosomes in the GnomAD database, including 99 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 0.017 (99 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.168

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.162 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: 0.0174 AC: 2654 AN: 152240 Hom.: 98 Cov.: 33

Gnomad AFR AF: 0.00306

Gnomad AMI AF: 0.0504

Gnomad AMR AF: 0.0140

Gnomad ASJ AF: 0.0124

Gnomad EAS AF: 0.171

Gnomad SAS AF: 0.0499

Gnomad FIN AF: 0.00809

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0143

Gnomad OTH AF: 0.0110

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

GnomAD4 genome AF: 0.0174 AC: 2657 AN: 152358 Hom.: 99 Cov.: 33 AF XY: 0.0190 AC XY: 1416 AN XY: 74500

Gnomad4 AFR AF: 0.00305

Gnomad4 AMR AF: 0.0140

Gnomad4 ASJ AF: 0.0124

Gnomad4 EAS AF: 0.171

Gnomad4 SAS AF: 0.0510

Gnomad4 FIN AF: 0.00809

Gnomad4 NFE AF: 0.0143

Gnomad4 OTH AF: 0.0109

Alfa AF: 0.0125 Hom.: 10

Bravo AF: 0.0178

Asia WGS AF: 0.0900 AC: 311 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	1.2
Dann	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10516747; hg19: chr4-86366112;