rs6750795

chr2-231513520-T-C

Variant summary

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

The NR_024079.1(LINC00471):n.364+7A>G variant causes a splice region, intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.579 in 534,400 control chromosomes in the GnomAD database, including 91,601 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 0.54 (22495 hom., cov: 32)
  • Exomes 𝑓: 0.60 (69106 hom.)
• Consequence: LINC00471 NR_024079.1 splice_region, intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.283

Genes affected

LINC00471 (HGNC:28668): (long intergenic non-protein coding RNA 471)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.707 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC00471	NR_024079.1	n.364+7A>G		splice_region_variant, intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00471	ENST00000313064.4	n.406+7A>G		splice_region_variant, intron_variant, non_coding_transcript_variant		1
LINC00471	ENST00000668648.2	n.410+7A>G		splice_region_variant, intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.536 AC: 81368 AN: 151914 Hom.: 22469 Cov.: 32

Gnomad AFR AF: 0.409

Gnomad AMI AF: 0.614

Gnomad AMR AF: 0.604

Gnomad ASJ AF: 0.716

Gnomad EAS AF: 0.726

Gnomad SAS AF: 0.693

Gnomad FIN AF: 0.567

Gnomad MID AF: 0.630

Gnomad NFE AF: 0.554

Gnomad OTH AF: 0.579

GnomAD3 exomes AF: 0.597 AC: 150093 AN: 251380 Hom.: 45651 AF XY: 0.601 AC XY: 81675 AN XY: 135870

Gnomad AFR exome AF: 0.399

Gnomad AMR exome AF: 0.664

Gnomad ASJ exome AF: 0.721

Gnomad EAS exome AF: 0.718

Gnomad SAS exome AF: 0.662

Gnomad FIN exome AF: 0.568

Gnomad NFE exome AF: 0.562

Gnomad OTH exome AF: 0.607

GnomAD4 exome AF: 0.597 AC: 228109 AN: 382368 Hom.: 69106 Cov.: 0 AF XY: 0.602 AC XY: 131126 AN XY: 217682

Gnomad4 AFR exome AF: 0.402

Gnomad4 AMR exome AF: 0.667

Gnomad4 ASJ exome AF: 0.717

Gnomad4 EAS exome AF: 0.720

Gnomad4 SAS exome AF: 0.659

Gnomad4 FIN exome AF: 0.569

Gnomad4 NFE exome AF: 0.561

Gnomad4 OTH exome AF: 0.592

GnomAD4 genome AF: 0.536 AC: 81428 AN: 152032 Hom.: 22495 Cov.: 32 AF XY: 0.541 AC XY: 40240 AN XY: 74320

Gnomad4 AFR AF: 0.409

Gnomad4 AMR AF: 0.605

Gnomad4 ASJ AF: 0.716

Gnomad4 EAS AF: 0.726

Gnomad4 SAS AF: 0.692

Gnomad4 FIN AF: 0.567

Gnomad4 NFE AF: 0.554

Gnomad4 OTH AF: 0.584

Alfa AF: 0.565 Hom.: 31731

Bravo AF: 0.533

Asia WGS AF: 0.737 AC: 2558 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	2.1
Dann	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6750795; hg19: chr2-232378231;