rs7317643

Variant names:

• chr13-107883680-C-T
• rs7317643
• ENST00000663056.1:n.104+14754C>T

Variant summary

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

The ENST00000663056.1(ENSG00000286343):​n.104+14754C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.155 in 152,052 control chromosomes in the GnomAD database, including 2,053 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 0.16 (2053 hom., cov: 32)
• Consequence: ENSG00000286343 ENST00000663056.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.430
• Publications: 2 publications found

Genes affected

ENSG00000286343 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.373 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000663056.1. 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
	ENSG00000286343	ENST00000663056.1		n.104+14754C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.155 AC: 23605 AN: 151934 Hom.: 2050 Cov.: 32

Gnomad AFR AF: 0.157

Gnomad AMI AF: 0.146

Gnomad AMR AF: 0.133

Gnomad ASJ AF: 0.0941

Gnomad EAS AF: 0.387

Gnomad SAS AF: 0.133

Gnomad FIN AF: 0.280

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.128

Gnomad OTH AF: 0.139

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

GnomAD4 genome AF: 0.155 AC: 23617 AN: 152052 Hom.: 2053 Cov.: 32 AF XY: 0.162 AC XY: 12011 AN XY: 74312

African (AFR) AF: 0.157 AC: 6502 AN: 41492

American (AMR) AF: 0.133 AC: 2029 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.0941 AC: 326 AN: 3466

East Asian (EAS) AF: 0.387 AC: 2001 AN: 5170

South Asian (SAS) AF: 0.133 AC: 639 AN: 4812

European-Finnish (FIN) AF: 0.280 AC: 2951 AN: 10542

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.128 AC: 8710 AN: 67988

Other (OTH) AF: 0.138 AC: 291 AN: 2114

Alfa AF: 0.134 Hom.: 1802

Bravo AF: 0.148

Asia WGS AF: 0.220 AC: 763 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	2.5
DANN	Benign	0.58
PhyloP100		0.43

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: rs7317643;

hg19: chr13-108536028;