rs1500237

Variant names:

• chr5-99279461-C-T
• rs1500237

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 0.305 in 151,942 control chromosomes in the GnomAD database, including 7,731 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 0.30 (7731 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.279
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.446 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: 0.305 AC: 46306 AN: 151824 Hom.: 7722 Cov.: 32

Gnomad AFR AF: 0.452

Gnomad AMI AF: 0.265

Gnomad AMR AF: 0.233

Gnomad ASJ AF: 0.279

Gnomad EAS AF: 0.198

Gnomad SAS AF: 0.285

Gnomad FIN AF: 0.282

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.247

Gnomad OTH AF: 0.289

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

GnomAD4 genome AF: 0.305 AC: 46337 AN: 151942 Hom.: 7731 Cov.: 32 AF XY: 0.302 AC XY: 22463 AN XY: 74260

African (AFR) AF: 0.452 AC: 18707 AN: 41432

American (AMR) AF: 0.233 AC: 3558 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.279 AC: 967 AN: 3466

East Asian (EAS) AF: 0.198 AC: 1025 AN: 5182

South Asian (SAS) AF: 0.285 AC: 1369 AN: 4810

European-Finnish (FIN) AF: 0.282 AC: 2977 AN: 10550

Middle Eastern (MID) AF: 0.289 AC: 85 AN: 294

European-Non Finnish (NFE) AF: 0.247 AC: 16798 AN: 67936

Other (OTH) AF: 0.290 AC: 610 AN: 2104

Alfa AF: 0.281 Hom.: 1115

Bravo AF: 0.309

Asia WGS AF: 0.263 AC: 914 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.3
DANN	Benign	0.74
PhyloP100		0.28

Splicing

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

Other links and lift over

dbSNP: rs1500237; hg19: chr5-98615165; COSMIC: COSV60169591;