chr2-181193801-T-C

Variant names:

• chr2-181193801-T-C
• rs4563183
• ENST00000424170.5:n.147-32670T>C

Variant summary

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

The ENST00000424170.5(LINC01934):​n.147-32670T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.486 in 151,998 control chromosomes in the GnomAD database, including 18,470 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 0.49 (18470 hom., cov: 32)
• Consequence: LINC01934 ENST00000424170.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.42
• Publications: 3 publications found

Genes affected

LINC01934 (HGNC:52757): (long intergenic non-protein coding RNA 1934)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.66 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01934	NR_130784.1	n.145-32670T>C		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01934	ENST00000424170.5	n.147-32670T>C		intron_variant	Intron 1 of 5	4
LINC01934	ENST00000424655.1	n.40-32670T>C		intron_variant	Intron 1 of 3	3
LINC01934	ENST00000428474.5	n.86-32670T>C		intron_variant	Intron 1 of 3	3

Frequencies

GnomAD3 genomes AF: 0.486 AC: 73822 AN: 151882 Hom.: 18445 Cov.: 32

Gnomad AFR AF: 0.510

Gnomad AMI AF: 0.580

Gnomad AMR AF: 0.556

Gnomad ASJ AF: 0.284

Gnomad EAS AF: 0.679

Gnomad SAS AF: 0.612

Gnomad FIN AF: 0.515

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.437

Gnomad OTH AF: 0.462

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

GnomAD4 genome AF: 0.486 AC: 73887 AN: 151998 Hom.: 18470 Cov.: 32 AF XY: 0.496 AC XY: 36843 AN XY: 74280

African (AFR) AF: 0.510 AC: 21127 AN: 41442

American (AMR) AF: 0.557 AC: 8493 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.284 AC: 986 AN: 3472

East Asian (EAS) AF: 0.679 AC: 3506 AN: 5164

South Asian (SAS) AF: 0.613 AC: 2959 AN: 4828

European-Finnish (FIN) AF: 0.515 AC: 5444 AN: 10566

Middle Eastern (MID) AF: 0.442 AC: 130 AN: 294

European-Non Finnish (NFE) AF: 0.437 AC: 29727 AN: 67956

Other (OTH) AF: 0.466 AC: 986 AN: 2114

Alfa AF: 0.483 Hom.: 3135

Bravo AF: 0.490

Asia WGS AF: 0.698 AC: 2424 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.44
DANN	Benign	0.38
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs4563183; hg19: chr2-182058528;