chr5-16009875-G-A

Variant names:

• chr5-16009875-G-A
• rs250503

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 0.257 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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	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

African (AFR) AF: 0.247 AC: 10258 AN: 41464

American (AMR) AF: 0.306 AC: 4662 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.183 AC: 636 AN: 3472

East Asian (EAS) AF: 0.650 AC: 3340 AN: 5136

South Asian (SAS) AF: 0.201 AC: 969 AN: 4814

European-Finnish (FIN) AF: 0.317 AC: 3342 AN: 10556

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.222 AC: 15099 AN: 67956

Other (OTH) AF: 0.246 AC: 520 AN: 2114

Alfa AF: 0.226 Hom.: 2119

Bravo AF: 0.260

Asia WGS AF: 0.353 AC: 1226 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	7.0
DANN	Benign	0.38
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs250503; hg19: chr5-16009984;