13-37290429-G-T

Variant names:

• chr13-37290429-G-T
• rs9315481
• ENST00000827668.1:n.233-16923G>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000827668.1(ENSG00000307651):​n.233-16923G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.906 in 152,052 control chromosomes in the GnomAD database, including 63,857 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 0.91 (63857 hom., cov: 31)
• Consequence: ENSG00000307651 ENST00000827668.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.861
• Publications: 1 publications found

Genes affected

ENSG00000307651 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.987 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
ENSG00000307651	ENST00000827668.1	n.233-16923G>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.907 AC: 137758 AN: 151934 Hom.: 63833 Cov.: 31

Gnomad AFR AF: 0.691

Gnomad AMI AF: 0.939

Gnomad AMR AF: 0.957

Gnomad ASJ AF: 0.995

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.987

Gnomad FIN AF: 1.00

Gnomad MID AF: 0.975

Gnomad NFE AF: 0.993

Gnomad OTH AF: 0.934

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

GnomAD4 genome AF: 0.906 AC: 137831 AN: 152052 Hom.: 63857 Cov.: 31 AF XY: 0.909 AC XY: 67628 AN XY: 74358

African (AFR) AF: 0.691 AC: 28608 AN: 41428

American (AMR) AF: 0.957 AC: 14615 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.995 AC: 3447 AN: 3466

East Asian (EAS) AF: 1.00 AC: 5156 AN: 5156

South Asian (SAS) AF: 0.988 AC: 4760 AN: 4820

European-Finnish (FIN) AF: 1.00 AC: 10600 AN: 10604

Middle Eastern (MID) AF: 0.976 AC: 285 AN: 292

European-Non Finnish (NFE) AF: 0.993 AC: 67532 AN: 67990

Other (OTH) AF: 0.935 AC: 1972 AN: 2110

Alfa AF: 0.942 Hom.: 8352

Bravo AF: 0.893

Asia WGS AF: 0.974 AC: 3388 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.62
DANN	Benign	0.52
PhyloP100		-0.86

Splicing

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

Other links and lift over

dbSNP: rs9315481; hg19: chr13-37864566;