rs10517364

Positions:

• chr4-35884836-C-T

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 0.311 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.323

Gnomad4 AMR AF: 0.289

Gnomad4 ASJ AF: 0.442

Gnomad4 EAS AF: 0.142

Gnomad4 SAS AF: 0.324

Gnomad4 FIN AF: 0.279

Gnomad4 NFE AF: 0.318

Gnomad4 OTH AF: 0.332

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10517364; hg19: chr4-35886458;