rs10515347

Positions:

• chr5-103587233-G-C
• chr5-103587233-G-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 0.334 in 151,730 control chromosomes in the GnomAD database, including 8,645 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 0.33 (8645 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.333

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.368 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: 0.334 AC: 50670 AN: 151610 Hom.: 8641 Cov.: 32

Gnomad AFR AF: 0.294

Gnomad AMI AF: 0.503

Gnomad AMR AF: 0.314

Gnomad ASJ AF: 0.383

Gnomad EAS AF: 0.181

Gnomad SAS AF: 0.349

Gnomad FIN AF: 0.317

Gnomad MID AF: 0.344

Gnomad NFE AF: 0.372

Gnomad OTH AF: 0.333

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

GnomAD4 genome AF: 0.334 AC: 50686 AN: 151730 Hom.: 8645 Cov.: 32 AF XY: 0.330 AC XY: 24419 AN XY: 74092

Gnomad4 AFR AF: 0.294

Gnomad4 AMR AF: 0.314

Gnomad4 ASJ AF: 0.383

Gnomad4 EAS AF: 0.180

Gnomad4 SAS AF: 0.348

Gnomad4 FIN AF: 0.317

Gnomad4 NFE AF: 0.372

Gnomad4 OTH AF: 0.333

Alfa AF: 0.212 Hom.: 457

Bravo AF: 0.332

Asia WGS AF: 0.263 AC: 909 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	7.3
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10515347; hg19: chr5-102922934;