13-38058441-A-C

Position:

• chr13-38058441-A-C

Variant summary

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

The NR_047500.1(LINC00571):​n.456+2955T>G variant causes a intron, non coding transcript 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 NR_047500.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.221

Genes affected

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

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

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC00571	NR_047500.1	n.456+2955T>G		intron_variant, non_coding_transcript_variant
LINC02334	XR_941880.4	n.760-6904A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC00571	ENST00000454060.2	n.812+2955T>G		intron_variant, non_coding_transcript_variant		3
LINC02334	ENST00000667295.1	n.710-6933A>C		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.395

Gnomad4 AMR AF: 0.525

Gnomad4 ASJ AF: 0.559

Gnomad4 EAS AF: 0.398

Gnomad4 SAS AF: 0.440

Gnomad4 FIN AF: 0.473

Gnomad4 NFE AF: 0.520

Gnomad4 OTH AF: 0.511

Alfa AF: 0.502 Hom.: 8299

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9315543; hg19: chr13-38632578;