rs9315443

Variant names:

• chr13-36737194-G-A
• rs9315443
• XR_001749824.2:n.594+15906C>T

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_001749824.2(LOC102723490):​n.594+15906C>T 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: LOC102723490 XR_001749824.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.178

Genes affected

LOC102723490 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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

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

Gnomad4 AFR AF: 0.362

Gnomad4 AMR AF: 0.234

Gnomad4 ASJ AF: 0.199

Gnomad4 EAS AF: 0.370

Gnomad4 SAS AF: 0.410

Gnomad4 FIN AF: 0.234

Gnomad4 NFE AF: 0.248

Gnomad4 OTH AF: 0.234

Alfa AF: 0.242 Hom.: 4597

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9315443; hg19: chr13-37311331;