13-37305031-C-T

Variant names:

• chr13-37305031-C-T
• rs1324038
• ENST00000827668.1:n.233-2321C>T

Variant summary

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

The ENST00000827668.1(ENSG00000307651):​n.233-2321C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.58 in 151,754 control chromosomes in the GnomAD database, including 25,669 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 0.58 (25669 hom., cov: 31)
• Consequence: ENSG00000307651 ENST00000827668.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.817
• Publications: 2 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 (SAS) allele frequency at 95% confidence interval = 0.647 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.233-2321C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.580 AC: 87922 AN: 151638 Hom.: 25659 Cov.: 31

Gnomad AFR AF: 0.524

Gnomad AMI AF: 0.508

Gnomad AMR AF: 0.521

Gnomad ASJ AF: 0.645

Gnomad EAS AF: 0.589

Gnomad SAS AF: 0.666

Gnomad FIN AF: 0.648

Gnomad MID AF: 0.628

Gnomad NFE AF: 0.607

Gnomad OTH AF: 0.599

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

GnomAD4 genome AF: 0.580 AC: 87968 AN: 151754 Hom.: 25669 Cov.: 31 AF XY: 0.580 AC XY: 43013 AN XY: 74156

African (AFR) AF: 0.523 AC: 21644 AN: 41366

American (AMR) AF: 0.521 AC: 7940 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.645 AC: 2239 AN: 3470

East Asian (EAS) AF: 0.588 AC: 3023 AN: 5138

South Asian (SAS) AF: 0.667 AC: 3212 AN: 4818

European-Finnish (FIN) AF: 0.648 AC: 6791 AN: 10478

Middle Eastern (MID) AF: 0.641 AC: 186 AN: 290

European-Non Finnish (NFE) AF: 0.607 AC: 41198 AN: 67918

Other (OTH) AF: 0.602 AC: 1272 AN: 2114

Alfa AF: 0.600 Hom.: 17210

Bravo AF: 0.565

Asia WGS AF: 0.631 AC: 2196 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	1.5
DANN	Benign	0.61
PhyloP100		-0.82

Splicing

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

Other links and lift over

dbSNP: rs1324038; hg19: chr13-37879168; COSMIC: COSV65945600;