rs2010338

chr14-46356678-T-C

Variant summary

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

The NR_102701.1(LINC00871):n.233-81503T>C 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 0.369 in 151,902 control chromosomes in the GnomAD database, including 10,950 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 0.37 (10950 hom., cov: 32)
• Consequence: LINC00871 NR_102701.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.01

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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.428 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC00871	NR_102701.1	n.233-81503T>C		intron_variant, non_coding_transcript_variant
LINC00871	NR_102702.1	n.233-144629T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00871	ENST00000666179.1	n.351-144629T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.369 AC: 55955 AN: 151784 Hom.: 10949 Cov.: 32

Gnomad AFR AF: 0.323

Gnomad AMI AF: 0.493

Gnomad AMR AF: 0.265

Gnomad ASJ AF: 0.381

Gnomad EAS AF: 0.0302

Gnomad SAS AF: 0.333

Gnomad FIN AF: 0.459

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.432

Gnomad OTH AF: 0.366

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

GnomAD4 genome AF: 0.369 AC: 55976 AN: 151902 Hom.: 10950 Cov.: 32 AF XY: 0.364 AC XY: 27061 AN XY: 74246

Gnomad4 AFR AF: 0.322

Gnomad4 AMR AF: 0.265

Gnomad4 ASJ AF: 0.381

Gnomad4 EAS AF: 0.0300

Gnomad4 SAS AF: 0.332

Gnomad4 FIN AF: 0.459

Gnomad4 NFE AF: 0.432

Gnomad4 OTH AF: 0.363

Alfa AF: 0.380 Hom.: 2198

Bravo AF: 0.350

Asia WGS AF: 0.184 AC: 644 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	4.4
Dann	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2010338; hg19: chr14-46825881;