rs11688631

Positions:

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

Variant summary

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

The ENST00000557729.2(LINC01956):​n.173+11488C>T 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 0.434 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 ENST00000557729.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.135

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01956	ENST00000557729.2	n.173+11488C>T		intron_variant, non_coding_transcript_variant		5

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

Gnomad4 AFR AF: 0.487

Gnomad4 AMR AF: 0.377

Gnomad4 ASJ AF: 0.340

Gnomad4 EAS AF: 0.135

Gnomad4 SAS AF: 0.294

Gnomad4 FIN AF: 0.458

Gnomad4 NFE AF: 0.449

Gnomad4 OTH AF: 0.422

Alfa AF: 0.396 Hom.: 2934

Bravo AF: 0.430

Asia WGS AF: 0.251 AC: 876 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11688631; hg19: chr2-119580435;