rs250503

Variant names:

• chr5-16009875-G-A
• rs250503

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 0.257 in 151,966 control chromosomes in the GnomAD database, including 5,611 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 0.26 (5611 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.197

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.632 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: 0.257 AC: 38987 AN: 151848 Hom.: 5613 Cov.: 32

Gnomad AFR AF: 0.247

Gnomad AMI AF: 0.161

Gnomad AMR AF: 0.306

Gnomad ASJ AF: 0.183

Gnomad EAS AF: 0.650

Gnomad SAS AF: 0.202

Gnomad FIN AF: 0.317

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.222

Gnomad OTH AF: 0.248

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

GnomAD4 genome AF: 0.257 AC: 39015 AN: 151966 Hom.: 5611 Cov.: 32 AF XY: 0.262 AC XY: 19445 AN XY: 74288

Gnomad4 AFR AF: 0.247

Gnomad4 AMR AF: 0.306

Gnomad4 ASJ AF: 0.183

Gnomad4 EAS AF: 0.650

Gnomad4 SAS AF: 0.201

Gnomad4 FIN AF: 0.317

Gnomad4 NFE AF: 0.222

Gnomad4 OTH AF: 0.246

Alfa AF: 0.226 Hom.: 1929

Bravo AF: 0.260

Asia WGS AF: 0.353 AC: 1226 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	7.0
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs250503; hg19: chr5-16009984;