rs6572335

chr14-45965382-A-G

Variant summary

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

The ENST00000666179.1(LINC00871):n.176+24364A>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 0.384 in 150,898 control chromosomes in the GnomAD database, including 12,666 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 0.38 (12666 hom., cov: 31)
• Consequence: LINC00871 ENST00000666179.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.540

Genes affected

LINC00871 (HGNC:47038): (long intergenic non-protein coding RNA 871)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.493 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00871	ENST00000666179.1	n.176+24364A>G		intron_variant, non_coding_transcript_variant
LINC00871	ENST00000555246.5	n.76+24364A>G		intron_variant, non_coding_transcript_variant		5
LINC00871	ENST00000664642.1	n.185+24364A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.385 AC: 57978 AN: 150780 Hom.: 12656 Cov.: 31

Gnomad AFR AF: 0.181

Gnomad AMI AF: 0.698

Gnomad AMR AF: 0.388

Gnomad ASJ AF: 0.447

Gnomad EAS AF: 0.248

Gnomad SAS AF: 0.381

Gnomad FIN AF: 0.464

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.497

Gnomad OTH AF: 0.406

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

GnomAD4 genome AF: 0.384 AC: 58003 AN: 150898 Hom.: 12666 Cov.: 31 AF XY: 0.382 AC XY: 28142 AN XY: 73662

Gnomad4 AFR AF: 0.182

Gnomad4 AMR AF: 0.387

Gnomad4 ASJ AF: 0.447

Gnomad4 EAS AF: 0.247

Gnomad4 SAS AF: 0.383

Gnomad4 FIN AF: 0.464

Gnomad4 NFE AF: 0.497

Gnomad4 OTH AF: 0.411

Alfa AF: 0.416 Hom.: 2371

Bravo AF: 0.370

Asia WGS AF: 0.311 AC: 1084 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	1.7
Dann	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6572335; hg19: chr14-46434585;