rs10516945

Variant names:

• chr4-94037465-T-C
• rs10516945

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 0.0585 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• 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

African (AFR) AF: 0.0144 AC: 599 AN: 41564

American (AMR) AF: 0.0454 AC: 694 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0358 AC: 124 AN: 3468

East Asian (EAS) AF: 0.000580 AC: 3 AN: 5174

South Asian (SAS) AF: 0.0188 AC: 91 AN: 4832

European-Finnish (FIN) AF: 0.118 AC: 1250 AN: 10578

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.0872 AC: 5930 AN: 67996

Other (OTH) AF: 0.0540 AC: 114 AN: 2112

Alfa AF: 0.0682 Hom.: 296

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
PhyloP100		-0.019

Splicing

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

Other links and lift over

dbSNP: rs10516945; hg19: chr4-94958616;