13-37910392-C-T

Variant names:

• chr13-37910392-C-T
• rs817737
• ENST00000838014.1:n.125+24517G>A

Variant summary

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

The ENST00000838014.1(ENSG00000309047):​n.125+24517G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.244 in 151,836 control chromosomes in the GnomAD database, including 6,072 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 0.24 (6072 hom., cov: 32)
• Consequence: ENSG00000309047 ENST00000838014.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.287
• Publications: 2 publications found

Genes affected

ENSG00000309047 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.461 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
ENSG00000309047	ENST00000838014.1	n.125+24517G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.244 AC: 37019 AN: 151718 Hom.: 6060 Cov.: 32

Gnomad AFR AF: 0.467

Gnomad AMI AF: 0.111

Gnomad AMR AF: 0.174

Gnomad ASJ AF: 0.172

Gnomad EAS AF: 0.184

Gnomad SAS AF: 0.203

Gnomad FIN AF: 0.127

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.156

Gnomad OTH AF: 0.236

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

GnomAD4 genome AF: 0.244 AC: 37064 AN: 151836 Hom.: 6072 Cov.: 32 AF XY: 0.241 AC XY: 17911 AN XY: 74230

African (AFR) AF: 0.467 AC: 19290 AN: 41340

American (AMR) AF: 0.174 AC: 2650 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.172 AC: 597 AN: 3464

East Asian (EAS) AF: 0.184 AC: 948 AN: 5158

South Asian (SAS) AF: 0.203 AC: 978 AN: 4820

European-Finnish (FIN) AF: 0.127 AC: 1347 AN: 10586

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.156 AC: 10596 AN: 67936

Other (OTH) AF: 0.235 AC: 493 AN: 2102

Alfa AF: 0.183 Hom.: 1425

Bravo AF: 0.255

Asia WGS AF: 0.184 AC: 641 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.8
DANN	Benign	0.80
PhyloP100		0.29

Splicing

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

Other links and lift over

dbSNP: rs817737; hg19: chr13-38484529;