rs10516945

Variant names:

• chr4-94037465-T-C
• rs10516945

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 0.0585 in 152,222 control chromosomes in the GnomAD database, including 360 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 0.058 (360 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0190

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0854 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: 0.0585 AC: 8897 AN: 152102 Hom.: 360 Cov.: 33

Gnomad AFR AF: 0.0145

Gnomad AMI AF: 0.0945

Gnomad AMR AF: 0.0454

Gnomad ASJ AF: 0.0358

Gnomad EAS AF: 0.000578

Gnomad SAS AF: 0.0186

Gnomad FIN AF: 0.118

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0872

Gnomad OTH AF: 0.0545

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

GnomAD4 genome AF: 0.0585 AC: 8898 AN: 152222 Hom.: 360 Cov.: 33 AF XY: 0.0597 AC XY: 4446 AN XY: 74420

Gnomad4 AFR AF: 0.0144

Gnomad4 AMR AF: 0.0454

Gnomad4 ASJ AF: 0.0358

Gnomad4 EAS AF: 0.000580

Gnomad4 SAS AF: 0.0188

Gnomad4 FIN AF: 0.118

Gnomad4 NFE AF: 0.0872

Gnomad4 OTH AF: 0.0540

Alfa AF: 0.0764 Hom.: 269

Bravo AF: 0.0499

Asia WGS AF: 0.0110 AC: 38 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.9
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10516945; hg19: chr4-94958616;