rs6750795

Variant names:

• chr2-231513520-T-C
• rs6750795
• ENST00000313064.5:n.407+7A>G

Variant summary

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

The ENST00000313064.5(LINC00471):​n.407+7A>G variant causes a splice region, intron 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 ENST00000313064.5 splice_region, intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.283
• Publications: 27 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LINC00471	NR_024079.1	n.364+7A>G		splice_region_variant, intron_variant	Intron 2 of 2
LINC00471	NR_199860.1	n.402+7A>G		splice_region_variant, intron_variant	Intron 2 of 5
LINC00471	NR_199861.1	n.402+7A>G		splice_region_variant, intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00471	ENST00000313064.5	n.407+7A>G		splice_region_variant, intron_variant	Intron 2 of 2	1
LINC00471	ENST00000750607.1	n.900A>G		non_coding_transcript_exon_variant	Exon 1 of 1
LINC00471	ENST00000750608.1	n.381A>G		non_coding_transcript_exon_variant	Exon 2 of 2

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

GnomAD2 exomes AF: 0.597 AC: 150093 AN: 251380 AF XY: 0.601

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 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

African (AFR) AF: 0.402 AC: 4227 AN: 10514

American (AMR) AF: 0.667 AC: 24211 AN: 36300

Ashkenazi Jewish (ASJ) AF: 0.717 AC: 8413 AN: 11740

East Asian (EAS) AF: 0.720 AC: 9485 AN: 13172

South Asian (SAS) AF: 0.659 AC: 43988 AN: 66752

European-Finnish (FIN) AF: 0.569 AC: 18357 AN: 32264

Middle Eastern (MID) AF: 0.641 AC: 1828 AN: 2854

European-Non Finnish (NFE) AF: 0.561 AC: 107695 AN: 192048

Other (OTH) AF: 0.592 AC: 9905 AN: 16724

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

African (AFR) AF: 0.409 AC: 16972 AN: 41466

American (AMR) AF: 0.605 AC: 9240 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.716 AC: 2483 AN: 3470

East Asian (EAS) AF: 0.726 AC: 3757 AN: 5174

South Asian (SAS) AF: 0.692 AC: 3338 AN: 4826

European-Finnish (FIN) AF: 0.567 AC: 5988 AN: 10552

Middle Eastern (MID) AF: 0.626 AC: 184 AN: 294

European-Non Finnish (NFE) AF: 0.554 AC: 37674 AN: 67952

Other (OTH) AF: 0.584 AC: 1233 AN: 2110

Alfa AF: 0.560 Hom.: 69328

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
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs6750795; hg19: chr2-232378231;