rs7962316

chr12-92026179-G-Achr12-92026179-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_132340.1(LINC01619):n.226-32650C>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 0.612 in 151,738 control chromosomes in the GnomAD database, including 29,277 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 0.61 (29277 hom., cov: 30)
• Consequence: LINC01619 NR_132340.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.301

Genes affected

LINC01619 (HGNC:27409): (long intergenic non-protein coding RNA 1619)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.973 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01619	NR_132340.1	n.226-32650C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01619	ENST00000549802.5	n.66-32650C>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.612 AC: 92764 AN: 151618 Hom.: 29252 Cov.: 30

Gnomad AFR AF: 0.496

Gnomad AMI AF: 0.678

Gnomad AMR AF: 0.607

Gnomad ASJ AF: 0.635

Gnomad EAS AF: 0.995

Gnomad SAS AF: 0.751

Gnomad FIN AF: 0.726

Gnomad MID AF: 0.659

Gnomad NFE AF: 0.624

Gnomad OTH AF: 0.621

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

GnomAD4 genome AF: 0.612 AC: 92839 AN: 151738 Hom.: 29277 Cov.: 30 AF XY: 0.621 AC XY: 46085 AN XY: 74158

Gnomad4 AFR AF: 0.496

Gnomad4 AMR AF: 0.607

Gnomad4 ASJ AF: 0.635

Gnomad4 EAS AF: 0.995

Gnomad4 SAS AF: 0.752

Gnomad4 FIN AF: 0.726

Gnomad4 NFE AF: 0.624

Gnomad4 OTH AF: 0.620

Alfa AF: 0.605 Hom.: 3834

Bravo AF: 0.596

Asia WGS AF: 0.804 AC: 2780 AN: 3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	0.84
Dann	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7962316; hg19: chr12-92419955;