2-10881605-T-G

Variant names:

• chr2-10881605-T-G
• rs4669638
• ENST00000607419.1:n.176+3161T>G

Variant summary

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

The ENST00000607419.1(LINC01954):​n.176+3161T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.224 in 152,196 control chromosomes in the GnomAD database, including 4,605 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 0.22 (4605 hom., cov: 33)
• Consequence: LINC01954 ENST00000607419.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.939
• Publications: 4 publications found

Genes affected

LINC01954 (HGNC:52779): (long intergenic non-protein coding RNA 1954)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.347 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000607419.1. 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
	LINC01954	NR_110575.1		n.178+3161T>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01954	ENST00000607419.1	TSL:1	n.176+3161T>G		intron	N/A
	LINC01954	ENST00000652896.2		n.475-3229T>G		intron	N/A
	LINC01954	ENST00000670239.2		n.446+3161T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.223 AC: 33951 AN: 152078 Hom.: 4581 Cov.: 33

Gnomad AFR AF: 0.348

Gnomad AMI AF: 0.145

Gnomad AMR AF: 0.225

Gnomad ASJ AF: 0.185

Gnomad EAS AF: 0.344

Gnomad SAS AF: 0.361

Gnomad FIN AF: 0.117

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.147

Gnomad OTH AF: 0.222

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

GnomAD4 genome AF: 0.224 AC: 34029 AN: 152196 Hom.: 4605 Cov.: 33 AF XY: 0.225 AC XY: 16724 AN XY: 74426

African (AFR) AF: 0.349 AC: 14483 AN: 41502

American (AMR) AF: 0.225 AC: 3449 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.185 AC: 641 AN: 3468

East Asian (EAS) AF: 0.344 AC: 1775 AN: 5166

South Asian (SAS) AF: 0.361 AC: 1745 AN: 4830

European-Finnish (FIN) AF: 0.117 AC: 1238 AN: 10612

Middle Eastern (MID) AF: 0.289 AC: 85 AN: 294

European-Non Finnish (NFE) AF: 0.147 AC: 10001 AN: 68004

Other (OTH) AF: 0.227 AC: 480 AN: 2112

Alfa AF: 0.159 Hom.: 1242

Bravo AF: 0.234

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.29
DANN	Benign	0.46
PhyloP100		-0.94

Splicing

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

Other links and lift over

dbSNP: rs4669638; hg19: chr2-11021731;