rs9315443

Variant names:

• chr13-36737194-G-A
• rs9315443
• ENST00000772969.1:n.257+1754G>A

Your query was ambiguous. Multiple possible variants found:

• chr13-36737194-G-A
• chr13-36737194-G-T

Variant summary

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

The ENST00000772969.1(ENSG00000293145):​n.257+1754G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.284 in 151,832 control chromosomes in the GnomAD database, including 6,430 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 0.28 (6430 hom., cov: 32)
• Consequence: ENSG00000293145 ENST00000772969.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.178
• Publications: 3 publications found

Genes affected

ENSG00000293145 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.395 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC102723490	XR_001749824.2	n.594+15906C>T		intron_variant	Intron 3 of 7
LOC102723490	XR_001749825.2	n.594+15906C>T		intron_variant	Intron 3 of 6
LOC102723490	XR_001749828.2	n.594+15906C>T		intron_variant	Intron 3 of 6
LOC102723490	XR_007063757.1	n.594+15906C>T		intron_variant	Intron 3 of 8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000293145	ENST00000772969.1	n.257+1754G>A		intron_variant	Intron 1 of 3
ENSG00000293145	ENST00000772970.1	n.108+1754G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.284 AC: 43039 AN: 151714 Hom.: 6411 Cov.: 32

Gnomad AFR AF: 0.362

Gnomad AMI AF: 0.178

Gnomad AMR AF: 0.233

Gnomad ASJ AF: 0.199

Gnomad EAS AF: 0.369

Gnomad SAS AF: 0.411

Gnomad FIN AF: 0.234

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.248

Gnomad OTH AF: 0.233

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

GnomAD4 genome AF: 0.284 AC: 43112 AN: 151832 Hom.: 6430 Cov.: 32 AF XY: 0.284 AC XY: 21089 AN XY: 74178

African (AFR) AF: 0.362 AC: 14995 AN: 41400

American (AMR) AF: 0.234 AC: 3560 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.199 AC: 691 AN: 3468

East Asian (EAS) AF: 0.370 AC: 1902 AN: 5144

South Asian (SAS) AF: 0.410 AC: 1979 AN: 4822

European-Finnish (FIN) AF: 0.234 AC: 2458 AN: 10512

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.248 AC: 16829 AN: 67934

Other (OTH) AF: 0.234 AC: 493 AN: 2110

Alfa AF: 0.247 Hom.: 6245

Bravo AF: 0.280

Asia WGS AF: 0.364 AC: 1263 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.7
DANN	Benign	0.80
PhyloP100		0.18

Splicing

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

Other links and lift over

dbSNP: rs9315443; hg19: chr13-37311331;