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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02689	XR_001748092.1	n.456+2464C>A		intron_variant	Intron 1 of 3
LINC02689	XR_930969.2	n.456+2464C>A		intron_variant	Intron 1 of 2
LINC02689	XR_930972.2	n.456+2464C>A		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02689	ENST00000650218.1	n.404+2464C>A		intron_variant	Intron 1 of 4

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 v4.3

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

Other links and lift over

dbSNP: rs7122936; hg19: chr11-1374456;