rs10516747

Variant names:

• chr4-85444959-A-G
• rs10516747

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 0.0174 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.00305 AC: 127 AN: 41586

American (AMR) AF: 0.0140 AC: 214 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.0124 AC: 43 AN: 3472

East Asian (EAS) AF: 0.171 AC: 889 AN: 5190

South Asian (SAS) AF: 0.0510 AC: 246 AN: 4828

European-Finnish (FIN) AF: 0.00809 AC: 86 AN: 10630

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.0143 AC: 970 AN: 68028

Other (OTH) AF: 0.0109 AC: 23 AN: 2112

Alfa AF: 0.0104 Hom.: 19

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
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs10516747; hg19: chr4-86366112;