rs11626637

chr14-46253459-A-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NR_102701.1(LINC00871):n.232+41655A>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 0.0667 in 152,228 control chromosomes in the GnomAD database, including 440 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 0.067 (440 hom., cov: 32)
• Consequence: LINC00871 NR_102701.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.97

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.46).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.1 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC00871	NR_102701.1	n.232+41655A>G		intron_variant, non_coding_transcript_variant
LINC00871	NR_102702.1	n.232+41655A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00871	ENST00000666179.1	n.350+41655A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0667 AC: 10153 AN: 152110 Hom.: 440 Cov.: 32

Gnomad AFR AF: 0.0184

Gnomad AMI AF: 0.0901

Gnomad AMR AF: 0.0571

Gnomad ASJ AF: 0.151

Gnomad EAS AF: 0.000579

Gnomad SAS AF: 0.0327

Gnomad FIN AF: 0.0571

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.102

Gnomad OTH AF: 0.0796

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

GnomAD4 genome AF: 0.0667 AC: 10157 AN: 152228 Hom.: 440 Cov.: 32 AF XY: 0.0634 AC XY: 4722 AN XY: 74430

Gnomad4 AFR AF: 0.0183

Gnomad4 AMR AF: 0.0569

Gnomad4 ASJ AF: 0.151

Gnomad4 EAS AF: 0.000580

Gnomad4 SAS AF: 0.0342

Gnomad4 FIN AF: 0.0571

Gnomad4 NFE AF: 0.102

Gnomad4 OTH AF: 0.0787

Alfa AF: 0.0891 Hom.: 341

Bravo AF: 0.0661

Asia WGS AF: 0.0190 AC: 68 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.46
Cadd	Benign	15
Dann	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11626637; hg19: chr14-46722662;