rs5014202

Variant names:

• chr15-66698193-T-C
• rs5014202

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 0.201 in 152,204 control chromosomes in the GnomAD database, including 3,337 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 0.20 (3337 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00300

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.335 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: 0.201 AC: 30562 AN: 152088 Hom.: 3328 Cov.: 32

Gnomad AFR AF: 0.166

Gnomad AMI AF: 0.168

Gnomad AMR AF: 0.343

Gnomad ASJ AF: 0.182

Gnomad EAS AF: 0.236

Gnomad SAS AF: 0.236

Gnomad FIN AF: 0.154

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.193

Gnomad OTH AF: 0.232

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

GnomAD4 genome AF: 0.201 AC: 30589 AN: 152204 Hom.: 3337 Cov.: 32 AF XY: 0.204 AC XY: 15196 AN XY: 74412

Gnomad4 AFR AF: 0.166

Gnomad4 AMR AF: 0.343

Gnomad4 ASJ AF: 0.182

Gnomad4 EAS AF: 0.235

Gnomad4 SAS AF: 0.236

Gnomad4 FIN AF: 0.154

Gnomad4 NFE AF: 0.193

Gnomad4 OTH AF: 0.234

Alfa AF: 0.203 Hom.: 364

Bravo AF: 0.216

Asia WGS AF: 0.227 AC: 791 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.0
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5014202; hg19: chr15-66990531;