rs917303

Positions:

• chr5-136082343-G-A

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 0.351 in 152,052 control chromosomes in the GnomAD database, including 9,458 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 0.35 (9458 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.160

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.478 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: 0.351 AC: 53254 AN: 151934 Hom.: 9449 Cov.: 33

Gnomad AFR AF: 0.354

Gnomad AMI AF: 0.306

Gnomad AMR AF: 0.358

Gnomad ASJ AF: 0.364

Gnomad EAS AF: 0.292

Gnomad SAS AF: 0.493

Gnomad FIN AF: 0.320

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.346

Gnomad OTH AF: 0.348

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

GnomAD4 genome AF: 0.351 AC: 53298 AN: 152052 Hom.: 9458 Cov.: 33 AF XY: 0.349 AC XY: 25900 AN XY: 74314

Gnomad4 AFR AF: 0.354

Gnomad4 AMR AF: 0.359

Gnomad4 ASJ AF: 0.364

Gnomad4 EAS AF: 0.292

Gnomad4 SAS AF: 0.494

Gnomad4 FIN AF: 0.320

Gnomad4 NFE AF: 0.346

Gnomad4 OTH AF: 0.345

Alfa AF: 0.358 Hom.: 4663

Bravo AF: 0.353

Asia WGS AF: 0.370 AC: 1284 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.4
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs917303; hg19: chr5-135418032;