6-31448759-A-G

Variant names:

• chr6-31448759-A-G
• rs2516463
• ENST00000673857.1:n.63-14364A>G

Variant summary

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

The ENST00000673857.1(ENSG00000288587):​n.63-14364A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.107 in 151,916 control chromosomes in the GnomAD database, including 1,318 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 0.11 (1318 hom., cov: 33)
• Consequence: ENSG00000288587 ENST00000673857.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.316
• Publications: 4 publications found

Genes affected

ENSG00000288587 (HGNC:):

LINC01149 (HGNC:39757): (long intergenic non-protein coding RNA 1149)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.19 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000673857.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000288587	ENST00000673857.1		n.63-14364A>G		intron	N/A
	LINC01149	ENST00000812003.1		n.*33A>G		downstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.107 AC: 16177 AN: 151798 Hom.: 1315 Cov.: 33

Gnomad AFR AF: 0.194

Gnomad AMI AF: 0.0329

Gnomad AMR AF: 0.125

Gnomad ASJ AF: 0.0838

Gnomad EAS AF: 0.0100

Gnomad SAS AF: 0.0858

Gnomad FIN AF: 0.0119

Gnomad MID AF: 0.105

Gnomad NFE AF: 0.0745

Gnomad OTH AF: 0.137

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

GnomAD4 genome AF: 0.107 AC: 16196 AN: 151916 Hom.: 1318 Cov.: 33 AF XY: 0.104 AC XY: 7692 AN XY: 74286

African (AFR) AF: 0.194 AC: 8008 AN: 41302

American (AMR) AF: 0.125 AC: 1895 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.0838 AC: 290 AN: 3462

East Asian (EAS) AF: 0.0102 AC: 53 AN: 5184

South Asian (SAS) AF: 0.0859 AC: 413 AN: 4810

European-Finnish (FIN) AF: 0.0119 AC: 126 AN: 10608

Middle Eastern (MID) AF: 0.0993 AC: 29 AN: 292

European-Non Finnish (NFE) AF: 0.0745 AC: 5067 AN: 68016

Other (OTH) AF: 0.135 AC: 285 AN: 2110

Alfa AF: 0.0828 Hom.: 656

Bravo AF: 0.121

Asia WGS AF: 0.0630 AC: 219 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	4.2
DANN	Benign	0.47
PhyloP100		0.32
Mutation Taster		=100/0	polymorphism (auto)

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: rs2516463;

hg19: chr6-31416536;