14-46356122-T-C

Variant names:

• chr14-46356122-T-C
• rs11625735
• ENST00000555246.5:n.299+37261T>C

Variant summary

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

The ENST00000556886.1(LINC00871):​n.233-82059T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.368 in 151,870 control chromosomes in the GnomAD database, including 10,911 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 (10911 hom., cov: 32)
• Consequence: LINC00871 ENST00000556886.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.185
• Publications: 5 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000556886.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00871	NR_102701.1		n.233-82059T>C		intron	N/A
	LINC00871	NR_102702.1		n.232+144318T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00871	ENST00000555246.5	TSL:5	n.299+37261T>C		intron	N/A
	LINC00871	ENST00000556886.1	TSL:3	n.233-82059T>C		intron	N/A
	LINC00871	ENST00000656720.1		n.233+144318T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.368 AC: 55862 AN: 151752 Hom.: 10910 Cov.: 32

Gnomad AFR AF: 0.323

Gnomad AMI AF: 0.493

Gnomad AMR AF: 0.265

Gnomad ASJ AF: 0.380

Gnomad EAS AF: 0.0296

Gnomad SAS AF: 0.322

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: 0.368 AC: 55882 AN: 151870 Hom.: 10911 Cov.: 32 AF XY: 0.363 AC XY: 26980 AN XY: 74224

African (AFR) AF: 0.323 AC: 13378 AN: 41456

American (AMR) AF: 0.265 AC: 4030 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.380 AC: 1317 AN: 3468

East Asian (EAS) AF: 0.0295 AC: 152 AN: 5160

South Asian (SAS) AF: 0.321 AC: 1547 AN: 4824

European-Finnish (FIN) AF: 0.459 AC: 4834 AN: 10542

Middle Eastern (MID) AF: 0.333 AC: 98 AN: 294

European-Non Finnish (NFE) AF: 0.432 AC: 29310 AN: 67872

Other (OTH) AF: 0.363 AC: 766 AN: 2112

Alfa AF: 0.285 Hom.: 1081

Bravo AF: 0.350

Asia WGS AF: 0.177 AC: 616 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.7
DANN	Benign	0.76
PhyloP100		-0.18

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs11625735;

hg19: chr14-46825325;