rs7317767

Variant names:

• chr13-106148682-C-T
• rs7317767
• ENST00000754737.1:n.129-57888G>A

Variant summary

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

The ENST00000754737.1(ENSG00000287923):​n.129-57888G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.561 in 146,698 control chromosomes in the GnomAD database, including 27,209 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 0.56 (27209 hom., cov: 25)
• Consequence: ENSG00000287923 ENST00000754737.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.39
• Publications: 2 publications found

Genes affected

ENSG00000287923 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.729 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
ENSG00000287923	ENST00000754737.1	n.129-57888G>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.561 AC: 82299 AN: 146600 Hom.: 27196 Cov.: 25

Gnomad AFR AF: 0.197

Gnomad AMI AF: 0.625

Gnomad AMR AF: 0.616

Gnomad ASJ AF: 0.615

Gnomad EAS AF: 0.541

Gnomad SAS AF: 0.659

Gnomad FIN AF: 0.741

Gnomad MID AF: 0.681

Gnomad NFE AF: 0.734

Gnomad OTH AF: 0.611

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

GnomAD4 genome AF: 0.561 AC: 82314 AN: 146698 Hom.: 27209 Cov.: 25 AF XY: 0.564 AC XY: 40023 AN XY: 70926

African (AFR) AF: 0.196 AC: 7930 AN: 40416

American (AMR) AF: 0.616 AC: 8698 AN: 14120

Ashkenazi Jewish (ASJ) AF: 0.615 AC: 2120 AN: 3448

East Asian (EAS) AF: 0.541 AC: 2648 AN: 4894

South Asian (SAS) AF: 0.659 AC: 3060 AN: 4646

European-Finnish (FIN) AF: 0.741 AC: 6647 AN: 8968

Middle Eastern (MID) AF: 0.681 AC: 188 AN: 276

European-Non Finnish (NFE) AF: 0.734 AC: 49231 AN: 67032

Other (OTH) AF: 0.615 AC: 1233 AN: 2004

Alfa AF: 0.682 Hom.: 153220

Bravo AF: 0.535

Asia WGS AF: 0.636 AC: 2207 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.29
DANN	Benign	0.54
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs7317767; hg19: chr13-106801031;