14-46488719-T-C

Position:

• chr14-46488719-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.350-12588T>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 0.597 in 151,690 control chromosomes in the GnomAD database, including 27,856 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 0.60 (27856 hom., cov: 30)
• Consequence: LINC00871 NR_102701.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.01

Genes affected

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

LOC124903309 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.18).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.907 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC00871	NR_102701.1	n.350-12588T>C		intron_variant, non_coding_transcript_variant
LOC124903309	XR_007064146.1	n.2464+478A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00871	ENST00000666179.1	n.351-12588T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.597 AC: 90478 AN: 151572 Hom.: 27848 Cov.: 30

Gnomad AFR AF: 0.547

Gnomad AMI AF: 0.686

Gnomad AMR AF: 0.432

Gnomad ASJ AF: 0.564

Gnomad EAS AF: 0.929

Gnomad SAS AF: 0.684

Gnomad FIN AF: 0.725

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.614

Gnomad OTH AF: 0.584

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

GnomAD4 genome AF: 0.597 AC: 90504 AN: 151690 Hom.: 27856 Cov.: 30 AF XY: 0.601 AC XY: 44536 AN XY: 74096

Gnomad4 AFR AF: 0.547

Gnomad4 AMR AF: 0.431

Gnomad4 ASJ AF: 0.564

Gnomad4 EAS AF: 0.929

Gnomad4 SAS AF: 0.682

Gnomad4 FIN AF: 0.725

Gnomad4 NFE AF: 0.614

Gnomad4 OTH AF: 0.585

Alfa AF: 0.610 Hom.: 12886

Bravo AF: 0.570

Asia WGS AF: 0.749 AC: 2607 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.2
CADD	Benign	0.014
DANN	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1389607; hg19: chr14-46957922;