rs7122936

Variant names:

• chr11-1353226-C-A
• rs7122936
• ENST00000650218.1:n.404+2464C>A

Your query was ambiguous. Multiple possible variants found:

• chr11-1353226-C-A
• chr11-1353226-C-G

Variant summary

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

The ENST00000650218.1(LINC02689):​n.404+2464C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.625 in 147,050 control chromosomes in the GnomAD database, including 28,971 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 0.63 (28971 hom., cov: 21)
• Consequence: LINC02689 ENST00000650218.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.509
• Publications: 5 publications found

Genes affected

LINC02689 (HGNC:54192): (long intergenic non-protein coding RNA 2689)

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 (AFR) allele frequency at 95% confidence interval = 0.677 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000650218.1. 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
	LINC02689	ENST00000650218.1		n.404+2464C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.625 AC: 91864 AN: 146926 Hom.: 28954 Cov.: 21

Gnomad AFR AF: 0.684

Gnomad AMI AF: 0.468

Gnomad AMR AF: 0.629

Gnomad ASJ AF: 0.621

Gnomad EAS AF: 0.606

Gnomad SAS AF: 0.681

Gnomad FIN AF: 0.538

Gnomad MID AF: 0.669

Gnomad NFE AF: 0.603

Gnomad OTH AF: 0.636

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

GnomAD4 genome AF: 0.625 AC: 91933 AN: 147050 Hom.: 28971 Cov.: 21 AF XY: 0.623 AC XY: 44554 AN XY: 71516

African (AFR) AF: 0.683 AC: 26941 AN: 39424

American (AMR) AF: 0.630 AC: 9265 AN: 14718

Ashkenazi Jewish (ASJ) AF: 0.621 AC: 2136 AN: 3442

East Asian (EAS) AF: 0.606 AC: 2897 AN: 4782

South Asian (SAS) AF: 0.681 AC: 3088 AN: 4532

European-Finnish (FIN) AF: 0.538 AC: 5379 AN: 9996

Middle Eastern (MID) AF: 0.672 AC: 195 AN: 290

European-Non Finnish (NFE) AF: 0.603 AC: 40322 AN: 66924

Other (OTH) AF: 0.631 AC: 1292 AN: 2048

Alfa AF: 0.610 Hom.: 47292

Bravo AF: 0.634

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.3
DANN	Benign	0.50
PhyloP100		0.51

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: rs7122936;

hg19: chr11-1374456;