rs9315542

Positions:

• chr13-38057334-T-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+4062A>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 0.257 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 NR_047500.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.148

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=-0.9).
• 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/exons	MANE	Protein	UniProt
LINC00571	NR_047500.1	n.456+4062A>G		intron_variant, non_coding_transcript_variant
LINC02334	XR_941880.4	n.760-8011T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC00571	ENST00000454060.2	n.813-3165A>G		intron_variant, non_coding_transcript_variant		3
LINC02334	ENST00000667295.1	n.710-8040T>C		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.190

Gnomad4 AMR AF: 0.225

Gnomad4 ASJ AF: 0.352

Gnomad4 EAS AF: 0.0412

Gnomad4 SAS AF: 0.240

Gnomad4 FIN AF: 0.227

Gnomad4 NFE AF: 0.319

Gnomad4 OTH AF: 0.278

Alfa AF: 0.287 Hom.: 1836

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9315542; hg19: chr13-38631471;