rs13202464

Variant names:

• chr6-31376806-A-G
• rs13202464
• ENST00000755446.1:n.327-5174A>G

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000755446.1(ENSG00000298426):​n.327-5174A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0655 in 152,240 control chromosomes in the GnomAD database, including 437 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 0.066 (437 hom., cov: 33)
• Consequence: ENSG00000298426 ENST00000755446.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.324
• Publications: 32 publications found

Genes affected

ENSG00000298426 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.37).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.131 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
ENSG00000298426	ENST00000755446.1	n.327-5174A>G		intron_variant	Intron 1 of 1
ENSG00000298474	ENST00000755731.1	n.304-1315T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0655 AC: 9959 AN: 152122 Hom.: 433 Cov.: 33

Gnomad AFR AF: 0.0185

Gnomad AMI AF: 0.0570

Gnomad AMR AF: 0.101

Gnomad ASJ AF: 0.0395

Gnomad EAS AF: 0.0925

Gnomad SAS AF: 0.140

Gnomad FIN AF: 0.112

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0734

Gnomad OTH AF: 0.0497

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

GnomAD4 genome AF: 0.0655 AC: 9979 AN: 152240 Hom.: 437 Cov.: 33 AF XY: 0.0703 AC XY: 5230 AN XY: 74434

African (AFR) AF: 0.0187 AC: 775 AN: 41520

American (AMR) AF: 0.102 AC: 1561 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0395 AC: 137 AN: 3470

East Asian (EAS) AF: 0.0929 AC: 482 AN: 5188

South Asian (SAS) AF: 0.140 AC: 677 AN: 4830

European-Finnish (FIN) AF: 0.112 AC: 1186 AN: 10598

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.0734 AC: 4990 AN: 68020

Other (OTH) AF: 0.0506 AC: 107 AN: 2114

Alfa AF: 0.0685 Hom.: 463

Bravo AF: 0.0595

Asia WGS AF: 0.150 AC: 524 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.37
CADD	Benign	13
DANN	Benign	0.95
PhyloP100		0.32

Splicing

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

Other links and lift over

dbSNP: rs13202464; hg19: chr6-31344583;