rs1502404

Variant names:

• chr15-37902554-G-A
• rs1502404

Your query was ambiguous. Multiple possible variants found:

• chr15-37902554-G-A
• chr15-37902554-G-C
• chr15-37902554-G-T

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 0.628 in 151,940 control chromosomes in the GnomAD database, including 30,394 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 0.63 (30394 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0570

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.831 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: 0.628 AC: 95381 AN: 151822 Hom.: 30355 Cov.: 32

Gnomad AFR AF: 0.694

Gnomad AMI AF: 0.512

Gnomad AMR AF: 0.568

Gnomad ASJ AF: 0.602

Gnomad EAS AF: 0.852

Gnomad SAS AF: 0.721

Gnomad FIN AF: 0.571

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.591

Gnomad OTH AF: 0.600

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

GnomAD4 genome AF: 0.628 AC: 95483 AN: 151940 Hom.: 30394 Cov.: 32 AF XY: 0.628 AC XY: 46625 AN XY: 74246

Gnomad4 AFR AF: 0.695

Gnomad4 AMR AF: 0.569

Gnomad4 ASJ AF: 0.602

Gnomad4 EAS AF: 0.852

Gnomad4 SAS AF: 0.721

Gnomad4 FIN AF: 0.571

Gnomad4 NFE AF: 0.591

Gnomad4 OTH AF: 0.601

Alfa AF: 0.600 Hom.: 55638

Bravo AF: 0.626

Asia WGS AF: 0.779 AC: 2709 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	1.6
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1502404; hg19: chr15-38194755;