rs11688631

Variant names:

• chr2-118822859-G-A
• rs11688631
• ENST00000557729.2:n.173+11488C>T

Your query was ambiguous. Multiple possible variants found:

• chr2-118822859-G-A
• chr2-118822859-G-T

Variant summary

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

The ENST00000806319.1(LINC01956):​n.557+11488C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.434 in 152,022 control chromosomes in the GnomAD database, including 14,707 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 0.43 (14707 hom., cov: 33)
• Consequence: LINC01956 ENST00000806319.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.135
• Publications: 2 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.481 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000806319.1. 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
	LINC01956	ENST00000557729.2	TSL:5	n.173+11488C>T		intron	N/A
	LINC01956	ENST00000806319.1		n.557+11488C>T		intron	N/A
	LINC01956	ENST00000806320.1		n.142+11488C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.434 AC: 65903 AN: 151904 Hom.: 14696 Cov.: 33

Gnomad AFR AF: 0.487

Gnomad AMI AF: 0.420

Gnomad AMR AF: 0.377

Gnomad ASJ AF: 0.340

Gnomad EAS AF: 0.135

Gnomad SAS AF: 0.295

Gnomad FIN AF: 0.458

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.449

Gnomad OTH AF: 0.421

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

GnomAD4 genome AF: 0.434 AC: 65963 AN: 152022 Hom.: 14707 Cov.: 33 AF XY: 0.429 AC XY: 31916 AN XY: 74318

African (AFR) AF: 0.487 AC: 20186 AN: 41468

American (AMR) AF: 0.377 AC: 5761 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.340 AC: 1176 AN: 3462

East Asian (EAS) AF: 0.135 AC: 698 AN: 5160

South Asian (SAS) AF: 0.294 AC: 1418 AN: 4818

European-Finnish (FIN) AF: 0.458 AC: 4836 AN: 10570

Middle Eastern (MID) AF: 0.279 AC: 82 AN: 294

European-Non Finnish (NFE) AF: 0.449 AC: 30535 AN: 67960

Other (OTH) AF: 0.422 AC: 889 AN: 2106

Alfa AF: 0.418 Hom.: 5899

Bravo AF: 0.430

Asia WGS AF: 0.251 AC: 876 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.52
DANN	Benign	0.42
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs11688631; hg19: chr2-119580435;