rs7122936

Positions:

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

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000650218.1(LINC02689):​n.404+2464C>A variant causes a intron, non coding transcript 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.509

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
LINC02689	XR_930969.2	n.456+2464C>A		intron_variant, non_coding_transcript_variant
LINC02689	XR_001748092.1	n.456+2464C>A		intron_variant, non_coding_transcript_variant
LINC02689	XR_930972.2	n.456+2464C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02689	ENST00000650218.1	n.404+2464C>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.683

Gnomad4 AMR AF: 0.630

Gnomad4 ASJ AF: 0.621

Gnomad4 EAS AF: 0.606

Gnomad4 SAS AF: 0.681

Gnomad4 FIN AF: 0.538

Gnomad4 NFE AF: 0.603

Gnomad4 OTH AF: 0.631

Alfa AF: 0.607 Hom.: 35551

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7122936; hg19: chr11-1374456;