rs11692564

Variant names:

• chr2-118788418-C-T
• rs11692564
• ENST00000557729.2:n.174-19979G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000557729.2(LINC01956):​n.174-19979G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0114 in 152,260 control chromosomes in the GnomAD database, including 14 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 0.011 (14 hom., cov: 32)
• Consequence: LINC01956 ENST00000557729.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.786
• Publications: 17 publications found

Genes affected

LINC01956 (HGNC:52777): (long intergenic non-protein coding RNA 1956)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0114 (1737/152260) while in subpopulation NFE AF = 0.0177 (1202/68024). AF 95% confidence interval is 0.0168. There are 14 homozygotes in GnomAd4. There are 853 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 14 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01956	ENST00000557729.2	n.174-19979G>A		intron_variant	Intron 2 of 3	5
LINC01956	ENST00000806319.1	n.558-21252G>A		intron_variant	Intron 2 of 2
LINC01956	ENST00000806320.1	n.143-19979G>A		intron_variant	Intron 2 of 3
LINC01956	ENST00000806321.1	n.667-361G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0114 AC: 1737 AN: 152140 Hom.: 14 Cov.: 32

Gnomad AFR AF: 0.00282

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.00805

Gnomad ASJ AF: 0.00692

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00498

Gnomad FIN AF: 0.0212

Gnomad MID AF: 0.00318

Gnomad NFE AF: 0.0177

Gnomad OTH AF: 0.00956

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

GnomAD4 genome AF: 0.0114 AC: 1737 AN: 152260 Hom.: 14 Cov.: 32 AF XY: 0.0115 AC XY: 853 AN XY: 74448

African (AFR) AF: 0.00282 AC: 117 AN: 41550

American (AMR) AF: 0.00804 AC: 123 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.00692 AC: 24 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5172

South Asian (SAS) AF: 0.00498 AC: 24 AN: 4820

European-Finnish (FIN) AF: 0.0212 AC: 225 AN: 10614

Middle Eastern (MID) AF: 0.00340 AC: 1 AN: 294

European-Non Finnish (NFE) AF: 0.0177 AC: 1202 AN: 68024

Other (OTH) AF: 0.00946 AC: 20 AN: 2114

Alfa AF: 0.0159 Hom.: 1

Bravo AF: 0.00990

Asia WGS AF: 0.00289 AC: 10 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.12
DANN	Benign	0.64
PhyloP100		-0.79

Splicing

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

Other links and lift over

dbSNP: rs11692564; hg19: chr2-119545994;