chr11-61057137-G-T

Variant names:

• chr11-61057137-G-T
• rs175110
• ENST00000536495.1:n.57+1344G>T

Variant summary

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

The ENST00000536495.1(LINC02954):​n.57+1344G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.312 in 151,966 control chromosomes in the GnomAD database, including 7,524 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 0.31 (7524 hom., cov: 32)
• Consequence: LINC02954 ENST00000536495.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0310
• Publications: 10 publications found

Genes affected

LINC02954 (HGNC:55972): (long intergenic non-protein coding RNA 2954)

ENSG00000303405 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.325 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000536495.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02954	NR_186234.1		n.231+1344G>T		intron	N/A
	LOC105369325	NR_188502.1		n.63-26742C>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02954	ENST00000536495.1	TSL:3	n.57+1344G>T		intron	N/A
	LINC02954	ENST00000659437.1		n.206+1344G>T		intron	N/A
	LINC02954	ENST00000664141.1		n.402+1344G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.312 AC: 47354 AN: 151848 Hom.: 7517 Cov.: 32

Gnomad AFR AF: 0.329

Gnomad AMI AF: 0.395

Gnomad AMR AF: 0.267

Gnomad ASJ AF: 0.252

Gnomad EAS AF: 0.286

Gnomad SAS AF: 0.333

Gnomad FIN AF: 0.276

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.319

Gnomad OTH AF: 0.333

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

GnomAD4 genome AF: 0.312 AC: 47397 AN: 151966 Hom.: 7524 Cov.: 32 AF XY: 0.310 AC XY: 23001 AN XY: 74262

African (AFR) AF: 0.329 AC: 13644 AN: 41440

American (AMR) AF: 0.266 AC: 4073 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.252 AC: 873 AN: 3464

East Asian (EAS) AF: 0.286 AC: 1480 AN: 5174

South Asian (SAS) AF: 0.333 AC: 1607 AN: 4820

European-Finnish (FIN) AF: 0.276 AC: 2913 AN: 10564

Middle Eastern (MID) AF: 0.310 AC: 91 AN: 294

European-Non Finnish (NFE) AF: 0.319 AC: 21662 AN: 67904

Other (OTH) AF: 0.330 AC: 695 AN: 2106

Alfa AF: 0.313 Hom.: 14714

Bravo AF: 0.314

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.15
DANN	Benign	0.58
PhyloP100		0.031

Splicing

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

Other links and lift over

dbSNP: rs175110; hg19: chr11-60824609;