rs9315543

Variant names:

• chr13-38058441-A-C
• rs9315543
• ENST00000434565.5:n.456+2955T>G

Your query was ambiguous. Multiple possible variants found:

• chr13-38058441-A-C
• chr13-38058441-A-G

Variant summary

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

The ENST00000434565.5(LINC00571):​n.456+2955T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.478 in 151,760 control chromosomes in the GnomAD database, including 17,719 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 0.48 (17719 hom., cov: 32)
• Consequence: LINC00571 ENST00000434565.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.221
• Publications: 3 publications found

Genes affected

LINC00571 (HGNC:43721): (long intergenic non-protein coding RNA 571)

LINC02334 (HGNC:53254): (long intergenic non-protein coding RNA 2334)

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 (AMR) allele frequency at 95% confidence interval = 0.515 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00571	NR_047500.1	n.456+2955T>G		intron_variant	Intron 5 of 5
LINC02334	XR_941880.4	n.760-6904A>C		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00571	ENST00000434565.5	n.456+2955T>G		intron_variant	Intron 5 of 5	3
LINC00571	ENST00000451826.2	n.948+1078T>G		intron_variant	Intron 7 of 7	2
LINC00571	ENST00000454060.2	n.812+2955T>G		intron_variant	Intron 7 of 7	3

Frequencies

GnomAD3 genomes AF: 0.478 AC: 72499 AN: 151644 Hom.: 17693 Cov.: 32

Gnomad AFR AF: 0.395

Gnomad AMI AF: 0.680

Gnomad AMR AF: 0.525

Gnomad ASJ AF: 0.559

Gnomad EAS AF: 0.398

Gnomad SAS AF: 0.437

Gnomad FIN AF: 0.473

Gnomad MID AF: 0.544

Gnomad NFE AF: 0.520

Gnomad OTH AF: 0.518

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

GnomAD4 genome AF: 0.478 AC: 72551 AN: 151760 Hom.: 17719 Cov.: 32 AF XY: 0.475 AC XY: 35204 AN XY: 74126

African (AFR) AF: 0.395 AC: 16333 AN: 41378

American (AMR) AF: 0.525 AC: 7993 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.559 AC: 1938 AN: 3470

East Asian (EAS) AF: 0.398 AC: 2055 AN: 5158

South Asian (SAS) AF: 0.440 AC: 2118 AN: 4818

European-Finnish (FIN) AF: 0.473 AC: 4966 AN: 10502

Middle Eastern (MID) AF: 0.558 AC: 164 AN: 294

European-Non Finnish (NFE) AF: 0.520 AC: 35292 AN: 67898

Other (OTH) AF: 0.511 AC: 1076 AN: 2106

Alfa AF: 0.504 Hom.: 9355

Bravo AF: 0.483

Asia WGS AF: 0.413 AC: 1436 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.52
DANN	Benign	0.65
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs9315543; hg19: chr13-38632578;