15-95585278-G-C

Variant names:

• chr15-95585278-G-C
• rs2397813
• ENST00000840556.1:n.380-6692G>C

Variant summary

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

The ENST00000840556.1(LINC00924):​n.380-6692G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.519 in 151,966 control chromosomes in the GnomAD database, including 23,032 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 0.52 (23032 hom., cov: 31)
• Consequence: LINC00924 ENST00000840556.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0430
• Publications: 0 publications found

Genes affected

LINC00924 (HGNC:27081): (long intergenic non-protein coding RNA 924)

ENSG00000309432 (HGNC:):

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 (AFR) allele frequency at 95% confidence interval = 0.791 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105370995	XR_932653.1	n.139-6692G>C		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00924	ENST00000840556.1	n.380-6692G>C		intron_variant	Intron 2 of 2
LINC00924	ENST00000840562.1	n.483-6692G>C		intron_variant	Intron 3 of 3
LINC00924	ENST00000840567.1	n.290-6692G>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.518 AC: 78721 AN: 151848 Hom.: 22984 Cov.: 31

Gnomad AFR AF: 0.798

Gnomad AMI AF: 0.593

Gnomad AMR AF: 0.455

Gnomad ASJ AF: 0.377

Gnomad EAS AF: 0.517

Gnomad SAS AF: 0.555

Gnomad FIN AF: 0.409

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.385

Gnomad OTH AF: 0.479

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

GnomAD4 genome AF: 0.519 AC: 78824 AN: 151966 Hom.: 23032 Cov.: 31 AF XY: 0.520 AC XY: 38606 AN XY: 74268

African (AFR) AF: 0.798 AC: 33122 AN: 41482

American (AMR) AF: 0.455 AC: 6933 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.377 AC: 1306 AN: 3466

East Asian (EAS) AF: 0.516 AC: 2656 AN: 5144

South Asian (SAS) AF: 0.553 AC: 2660 AN: 4806

European-Finnish (FIN) AF: 0.409 AC: 4316 AN: 10552

Middle Eastern (MID) AF: 0.401 AC: 118 AN: 294

European-Non Finnish (NFE) AF: 0.385 AC: 26167 AN: 67942

Other (OTH) AF: 0.475 AC: 1005 AN: 2114

Alfa AF: 0.256 Hom.: 518

Bravo AF: 0.536

Asia WGS AF: 0.554 AC: 1928 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	1.3
DANN	Benign	0.32
PhyloP100		-0.043

Splicing

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

Other links and lift over

dbSNP: rs2397813; hg19: chr15-96128507;