rs16985798

Variant names:

• chr2-18991213-G-A
• rs16985798
• ENST00000424895.1:n.532-3345C>T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000424895.1(LINC01376):​n.532-3345C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.457 in 151,870 control chromosomes in the GnomAD database, including 17,111 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 0.46 (17111 hom., cov: 32)
• Consequence: LINC01376 ENST00000424895.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.34
• Publications: 3 publications found

Genes affected

LINC01376 (HGNC:50637): (long intergenic non-protein coding RNA 1376)

ENSG00000287284 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.39).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.838 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01376	NR_135287.1	n.532-3345C>T		intron_variant	Intron 3 of 3
LOC105373456	XR_007086234.1	n.1138+71836G>A		intron_variant	Intron 5 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01376	ENST00000424895.1	n.532-3345C>T		intron_variant	Intron 3 of 3	2
LINC01376	ENST00000432142.6	n.956-3345C>T		intron_variant	Intron 5 of 5	4
LINC01376	ENST00000650025.1	n.686-3345C>T		intron_variant	Intron 7 of 7

Frequencies

GnomAD3 genomes AF: 0.456 AC: 69247 AN: 151752 Hom.: 17068 Cov.: 32

Gnomad AFR AF: 0.589

Gnomad AMI AF: 0.330

Gnomad AMR AF: 0.432

Gnomad ASJ AF: 0.437

Gnomad EAS AF: 0.859

Gnomad SAS AF: 0.569

Gnomad FIN AF: 0.311

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.368

Gnomad OTH AF: 0.451

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

GnomAD4 genome AF: 0.457 AC: 69350 AN: 151870 Hom.: 17111 Cov.: 32 AF XY: 0.457 AC XY: 33951 AN XY: 74220

African (AFR) AF: 0.589 AC: 24381 AN: 41390

American (AMR) AF: 0.432 AC: 6602 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.437 AC: 1515 AN: 3466

East Asian (EAS) AF: 0.859 AC: 4432 AN: 5158

South Asian (SAS) AF: 0.570 AC: 2744 AN: 4810

European-Finnish (FIN) AF: 0.311 AC: 3279 AN: 10538

Middle Eastern (MID) AF: 0.449 AC: 132 AN: 294

European-Non Finnish (NFE) AF: 0.368 AC: 25005 AN: 67936

Other (OTH) AF: 0.457 AC: 960 AN: 2102

Alfa AF: 0.398 Hom.: 16054

Bravo AF: 0.468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.39
CADD	Benign	17
PhyloP100		3.3

Splicing

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

Other links and lift over

dbSNP: rs16985798; hg19: chr2-19172488;