rs1500251

Variant names:

• chr5-99257749-G-A
• rs1500251

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 0.209 in 152,106 control chromosomes in the GnomAD database, including 3,426 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 0.21 (3426 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0400
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.31 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: 0.209 AC: 31765 AN: 151986 Hom.: 3428 Cov.: 32

Gnomad AFR AF: 0.217

Gnomad AMI AF: 0.210

Gnomad AMR AF: 0.214

Gnomad ASJ AF: 0.210

Gnomad EAS AF: 0.160

Gnomad SAS AF: 0.324

Gnomad FIN AF: 0.153

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.206

Gnomad OTH AF: 0.227

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

GnomAD4 genome AF: 0.209 AC: 31781 AN: 152106 Hom.: 3426 Cov.: 32 AF XY: 0.209 AC XY: 15555 AN XY: 74376

African (AFR) AF: 0.217 AC: 9005 AN: 41482

American (AMR) AF: 0.214 AC: 3269 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.210 AC: 729 AN: 3466

East Asian (EAS) AF: 0.160 AC: 829 AN: 5174

South Asian (SAS) AF: 0.324 AC: 1558 AN: 4816

European-Finnish (FIN) AF: 0.153 AC: 1619 AN: 10590

Middle Eastern (MID) AF: 0.262 AC: 77 AN: 294

European-Non Finnish (NFE) AF: 0.206 AC: 14029 AN: 67982

Other (OTH) AF: 0.225 AC: 475 AN: 2110

Alfa AF: 0.210 Hom.: 14791

Bravo AF: 0.209

Asia WGS AF: 0.227 AC: 790 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	3.1
DANN	Benign	0.30
PhyloP100		0.040

Splicing

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

Other links and lift over

dbSNP: rs1500251; hg19: chr5-98593453;