rs7115456

Variant names:

• chr11-44693132-C-G
• rs7115456
• ENST00000793366.1:n.329+3089G>C

Your query was ambiguous. Multiple possible variants found:

• chr11-44693132-C-G
• chr11-44693132-C-T

Variant summary

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

The ENST00000793366.1(LINC02704):​n.329+3089G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.456 in 151,678 control chromosomes in the GnomAD database, including 18,961 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 0.46 (18961 hom., cov: 32)
• Consequence: LINC02704 ENST00000793366.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.123
• Publications: 2 publications found

Genes affected

LINC02704 (HGNC:54220): (long intergenic non-protein coding RNA 2704)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.624 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000793366.1. 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
	LINC02704	ENST00000793366.1		n.329+3089G>C		intron	N/A
	LINC02704	ENST00000793367.1		n.288+3089G>C		intron	N/A
	LINC02704	ENST00000793368.1		n.526+1723G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.457 AC: 69198 AN: 151558 Hom.: 18969 Cov.: 32

Gnomad AFR AF: 0.173

Gnomad AMI AF: 0.398

Gnomad AMR AF: 0.408

Gnomad ASJ AF: 0.572

Gnomad EAS AF: 0.149

Gnomad SAS AF: 0.501

Gnomad FIN AF: 0.622

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.629

Gnomad OTH AF: 0.473

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

GnomAD4 genome AF: 0.456 AC: 69165 AN: 151678 Hom.: 18961 Cov.: 32 AF XY: 0.451 AC XY: 33444 AN XY: 74096

African (AFR) AF: 0.173 AC: 7166 AN: 41478

American (AMR) AF: 0.407 AC: 6211 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.572 AC: 1980 AN: 3462

East Asian (EAS) AF: 0.149 AC: 771 AN: 5172

South Asian (SAS) AF: 0.503 AC: 2418 AN: 4810

European-Finnish (FIN) AF: 0.622 AC: 6509 AN: 10462

Middle Eastern (MID) AF: 0.466 AC: 136 AN: 292

European-Non Finnish (NFE) AF: 0.629 AC: 42633 AN: 67748

Other (OTH) AF: 0.466 AC: 981 AN: 2104

Alfa AF: 0.415 Hom.: 1413

Bravo AF: 0.427

Asia WGS AF: 0.310 AC: 1080 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.1
DANN	Benign	0.63
PhyloP100		-0.12

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: rs7115456;

hg19: chr11-44714682;