13-75017368-T-C

Variant names:

• chr13-75017368-T-C
• rs9318312
• ENST00000807127.1:n.110+5145A>G

Variant summary

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

The ENST00000807127.1(ENSG00000304923):​n.110+5145A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.52 in 151,970 control chromosomes in the GnomAD database, including 21,273 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 0.52 (21273 hom., cov: 31)
• Consequence: ENSG00000304923 ENST00000807127.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.457
• Publications: 5 publications found

Genes affected

ENSG00000304923 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.58 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000807127.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000304923	ENST00000807127.1		n.110+5145A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.520 AC: 79015 AN: 151852 Hom.: 21261 Cov.: 31

Gnomad AFR AF: 0.377

Gnomad AMI AF: 0.620

Gnomad AMR AF: 0.565

Gnomad ASJ AF: 0.576

Gnomad EAS AF: 0.564

Gnomad SAS AF: 0.439

Gnomad FIN AF: 0.586

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.585

Gnomad OTH AF: 0.536

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

GnomAD4 genome AF: 0.520 AC: 79063 AN: 151970 Hom.: 21273 Cov.: 31 AF XY: 0.520 AC XY: 38620 AN XY: 74270

African (AFR) AF: 0.378 AC: 15653 AN: 41438

American (AMR) AF: 0.564 AC: 8615 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.576 AC: 1997 AN: 3470

East Asian (EAS) AF: 0.563 AC: 2907 AN: 5162

South Asian (SAS) AF: 0.438 AC: 2107 AN: 4808

European-Finnish (FIN) AF: 0.586 AC: 6186 AN: 10556

Middle Eastern (MID) AF: 0.524 AC: 154 AN: 294

European-Non Finnish (NFE) AF: 0.585 AC: 39742 AN: 67958

Other (OTH) AF: 0.539 AC: 1138 AN: 2110

Alfa AF: 0.506 Hom.: 4169

Bravo AF: 0.516

Asia WGS AF: 0.530 AC: 1839 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.8
DANN	Benign	0.64
PhyloP100		-0.46

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs9318312;

hg19: chr13-75591505;

COSMIC: COSV62693138;