rs16985798

Positions:

• chr2-18991213-G-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NR_135287.1(LINC01376):​n.532-3345C>T variant causes a intron, non coding transcript 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 NR_135287.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.34

Genes affected

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

LOC105373456 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LINC01376	NR_135287.1	n.532-3345C>T		intron_variant, non_coding_transcript_variant
LOC105373456	XR_007086234.1	n.1138+71836G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01376	ENST00000650025.1	n.686-3345C>T		intron_variant, non_coding_transcript_variant
LINC01376	ENST00000424895.1	n.532-3345C>T		intron_variant, non_coding_transcript_variant		2

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

Gnomad4 AFR AF: 0.589

Gnomad4 AMR AF: 0.432

Gnomad4 ASJ AF: 0.437

Gnomad4 EAS AF: 0.859

Gnomad4 SAS AF: 0.570

Gnomad4 FIN AF: 0.311

Gnomad4 NFE AF: 0.368

Gnomad4 OTH AF: 0.457

Alfa AF: 0.391 Hom.: 11807

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16985798; hg19: chr2-19172488;