rs917303

Variant names:

• chr5-136082343-G-A
• rs917303

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 0.351 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
• Publications: 8 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.354 AC: 14656 AN: 41450

American (AMR) AF: 0.359 AC: 5482 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.364 AC: 1262 AN: 3468

East Asian (EAS) AF: 0.292 AC: 1513 AN: 5176

South Asian (SAS) AF: 0.494 AC: 2383 AN: 4820

European-Finnish (FIN) AF: 0.320 AC: 3374 AN: 10558

Middle Eastern (MID) AF: 0.333 AC: 98 AN: 294

European-Non Finnish (NFE) AF: 0.346 AC: 23522 AN: 67980

Other (OTH) AF: 0.345 AC: 729 AN: 2112

Alfa AF: 0.358 Hom.: 5189

Bravo AF: 0.353

Asia WGS AF: 0.370 AC: 1284 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.4
DANN	Benign	0.66
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs917303; hg19: chr5-135418032;