rs10517364

Variant names:

• chr4-35884836-C-T
• rs10517364

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 0.311 in 151,920 control chromosomes in the GnomAD database, including 7,469 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 0.31 (7469 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.562
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.318 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: 0.311 AC: 47273 AN: 151802 Hom.: 7464 Cov.: 32

Gnomad AFR AF: 0.323

Gnomad AMI AF: 0.369

Gnomad AMR AF: 0.289

Gnomad ASJ AF: 0.442

Gnomad EAS AF: 0.142

Gnomad SAS AF: 0.324

Gnomad FIN AF: 0.279

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.318

Gnomad OTH AF: 0.333

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

GnomAD4 genome AF: 0.311 AC: 47319 AN: 151920 Hom.: 7469 Cov.: 32 AF XY: 0.309 AC XY: 22908 AN XY: 74248

African (AFR) AF: 0.323 AC: 13373 AN: 41442

American (AMR) AF: 0.289 AC: 4406 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.442 AC: 1534 AN: 3468

East Asian (EAS) AF: 0.142 AC: 732 AN: 5156

South Asian (SAS) AF: 0.324 AC: 1563 AN: 4826

European-Finnish (FIN) AF: 0.279 AC: 2945 AN: 10554

Middle Eastern (MID) AF: 0.405 AC: 119 AN: 294

European-Non Finnish (NFE) AF: 0.318 AC: 21611 AN: 67928

Other (OTH) AF: 0.332 AC: 700 AN: 2110

Alfa AF: 0.309 Hom.: 1249

Bravo AF: 0.313

Asia WGS AF: 0.265 AC: 921 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.070
DANN	Benign	0.42
PhyloP100		-0.56

Splicing

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

Other links and lift over

dbSNP: rs10517364; hg19: chr4-35886458;