chr13-38057334-T-C

Variant names:

• chr13-38057334-T-C
• rs9315542
• ENST00000434565.5:n.456+4062A>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+4062A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.257 in 152,186 control chromosomes in the GnomAD database, including 5,491 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 0.26 (5491 hom., cov: 32)
• Consequence: LINC00571 ENST00000434565.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.148
• Publications: 6 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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.316 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00571	NR_047500.1	n.456+4062A>G		intron_variant	Intron 5 of 5
LINC02334	XR_941880.4	n.760-8011T>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+4062A>G		intron_variant	Intron 5 of 5	3
LINC00571	ENST00000451826.2	n.948+2185A>G		intron_variant	Intron 7 of 7	2
LINC00571	ENST00000454060.2	n.813-3165A>G		intron_variant	Intron 7 of 7	3

Frequencies

GnomAD3 genomes AF: 0.257 AC: 39107 AN: 152068 Hom.: 5489 Cov.: 32

Gnomad AFR AF: 0.190

Gnomad AMI AF: 0.451

Gnomad AMR AF: 0.225

Gnomad ASJ AF: 0.352

Gnomad EAS AF: 0.0412

Gnomad SAS AF: 0.240

Gnomad FIN AF: 0.227

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.319

Gnomad OTH AF: 0.283

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

GnomAD4 genome AF: 0.257 AC: 39113 AN: 152186 Hom.: 5491 Cov.: 32 AF XY: 0.249 AC XY: 18534 AN XY: 74408

African (AFR) AF: 0.190 AC: 7872 AN: 41540

American (AMR) AF: 0.225 AC: 3432 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.352 AC: 1223 AN: 3470

East Asian (EAS) AF: 0.0412 AC: 214 AN: 5188

South Asian (SAS) AF: 0.240 AC: 1160 AN: 4828

European-Finnish (FIN) AF: 0.227 AC: 2405 AN: 10580

Middle Eastern (MID) AF: 0.323 AC: 95 AN: 294

European-Non Finnish (NFE) AF: 0.319 AC: 21714 AN: 67980

Other (OTH) AF: 0.278 AC: 587 AN: 2114

Alfa AF: 0.285 Hom.: 1857

Bravo AF: 0.258

Asia WGS AF: 0.130 AC: 454 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.87
DANN	Benign	0.85
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs9315542; hg19: chr13-38631471;