rs1502404

Variant names:

• chr15-37902554-G-A
• rs1502404
• ENST00000772735.1:n.387+1793C>T

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. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000772735.1(ENSG00000300563):​n.387+1793C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: ENSG00000300563 ENST00000772735.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0570
• Publications: 3 publications found

Genes affected

ENSG00000300563 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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
ENSG00000300563	ENST00000772735.1	n.387+1793C>T		intron_variant	Intron 3 of 4
ENSG00000300563	ENST00000772736.1	n.354+1793C>T		intron_variant	Intron 3 of 4
ENSG00000300563	ENST00000772737.1	n.424+1793C>T		intron_variant	Intron 3 of 5

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

African (AFR) AF: 0.695 AC: 28789 AN: 41436

American (AMR) AF: 0.569 AC: 8676 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.602 AC: 2089 AN: 3472

East Asian (EAS) AF: 0.852 AC: 4386 AN: 5148

South Asian (SAS) AF: 0.721 AC: 3476 AN: 4820

European-Finnish (FIN) AF: 0.571 AC: 6036 AN: 10562

Middle Eastern (MID) AF: 0.561 AC: 165 AN: 294

European-Non Finnish (NFE) AF: 0.591 AC: 40134 AN: 67942

Other (OTH) AF: 0.601 AC: 1267 AN: 2108

Alfa AF: 0.607 Hom.: 120355

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
PhyloP100		0.057

Splicing

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

Other links and lift over

dbSNP: rs1502404; hg19: chr15-38194755;