ENST00000532380.3:n.305+5401G>C

Variant names:

• chr11-22474672-C-G
• rs340989
• ENST00000532380.3:n.305+5401G>C

Variant summary

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

The ENST00000532380.3(LINC01495):​n.305+5401G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.536 in 151,558 control chromosomes in the GnomAD database, including 23,962 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 0.54 (23962 hom., cov: 31)
• Consequence: LINC01495 ENST00000532380.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.125
• Publications: 2 publications found

Genes affected

LINC01495 (HGNC:51161): (long intergenic non-protein coding RNA 1495)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.701 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01495	NR_120583.1	n.242+5401G>C		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01495	ENST00000532380.3	n.305+5401G>C		intron_variant	Intron 2 of 3	2
LINC01495	ENST00000534135.6	n.270+5401G>C		intron_variant	Intron 2 of 4	2
LINC01495	ENST00000653021.2	n.305+5401G>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.536 AC: 81144 AN: 151442 Hom.: 23954 Cov.: 31

Gnomad AFR AF: 0.261

Gnomad AMI AF: 0.682

Gnomad AMR AF: 0.646

Gnomad ASJ AF: 0.528

Gnomad EAS AF: 0.720

Gnomad SAS AF: 0.578

Gnomad FIN AF: 0.684

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.636

Gnomad OTH AF: 0.558

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

GnomAD4 genome AF: 0.536 AC: 81176 AN: 151558 Hom.: 23962 Cov.: 31 AF XY: 0.542 AC XY: 40137 AN XY: 74034

African (AFR) AF: 0.261 AC: 10807 AN: 41376

American (AMR) AF: 0.646 AC: 9820 AN: 15192

Ashkenazi Jewish (ASJ) AF: 0.528 AC: 1824 AN: 3454

East Asian (EAS) AF: 0.720 AC: 3698 AN: 5136

South Asian (SAS) AF: 0.579 AC: 2791 AN: 4820

European-Finnish (FIN) AF: 0.684 AC: 7219 AN: 10550

Middle Eastern (MID) AF: 0.507 AC: 148 AN: 292

European-Non Finnish (NFE) AF: 0.636 AC: 43082 AN: 67722

Other (OTH) AF: 0.554 AC: 1168 AN: 2108

Alfa AF: 0.488 Hom.: 1697

Bravo AF: 0.520

Asia WGS AF: 0.585 AC: 2036 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.8
DANN	Benign	0.30
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs340989; hg19: chr11-22496218;