rs10517809

Variant names:

• chr4-164578126-C-T
• rs10517809

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 0.838 in 152,152 control chromosomes in the GnomAD database, including 55,942 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 0.84 (55942 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.607
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.956 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: 0.838 AC: 127416 AN: 152034 Hom.: 55939 Cov.: 32

Gnomad AFR AF: 0.552

Gnomad AMI AF: 0.997

Gnomad AMR AF: 0.913

Gnomad ASJ AF: 0.957

Gnomad EAS AF: 0.765

Gnomad SAS AF: 0.951

Gnomad FIN AF: 0.973

Gnomad MID AF: 0.915

Gnomad NFE AF: 0.962

Gnomad OTH AF: 0.864

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

GnomAD4 genome AF: 0.838 AC: 127463 AN: 152152 Hom.: 55942 Cov.: 32 AF XY: 0.842 AC XY: 62600 AN XY: 74386

African (AFR) AF: 0.552 AC: 22882 AN: 41436

American (AMR) AF: 0.913 AC: 13955 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.957 AC: 3323 AN: 3472

East Asian (EAS) AF: 0.765 AC: 3953 AN: 5170

South Asian (SAS) AF: 0.951 AC: 4586 AN: 4824

European-Finnish (FIN) AF: 0.973 AC: 10331 AN: 10614

Middle Eastern (MID) AF: 0.908 AC: 267 AN: 294

European-Non Finnish (NFE) AF: 0.962 AC: 65454 AN: 68038

Other (OTH) AF: 0.855 AC: 1803 AN: 2110

Alfa AF: 0.930 Hom.: 110632

Bravo AF: 0.822

Asia WGS AF: 0.799 AC: 2780 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.5
DANN	Benign	0.76
PhyloP100		-0.61

Splicing

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

Other links and lift over

dbSNP: rs10517809; hg19: chr4-165499278;