rs337663

Positions:

• chr12-92311428-A-G

Variant summary

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

The ENST00000615716.2(LINC02391):​n.387-38812T>C 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 0.578 in 152,128 control chromosomes in the GnomAD database, including 26,318 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 0.58 (26318 hom., cov: 32)
• Consequence: LINC02391 ENST00000615716.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09

Genes affected

LINC02391 (HGNC:53318): (long intergenic non-protein coding RNA 2391)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.729 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02391	XR_007063404.1	n.387-42449T>C		intron_variant, non_coding_transcript_variant
LINC02391	XR_007063403.1	n.387-22821T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02391	ENST00000615716.2	n.387-38812T>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.578 AC: 87922 AN: 152010 Hom.: 26296 Cov.: 32

Gnomad AFR AF: 0.736

Gnomad AMI AF: 0.496

Gnomad AMR AF: 0.459

Gnomad ASJ AF: 0.583

Gnomad EAS AF: 0.633

Gnomad SAS AF: 0.458

Gnomad FIN AF: 0.511

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.526

Gnomad OTH AF: 0.568

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

GnomAD4 genome AF: 0.578 AC: 87995 AN: 152128 Hom.: 26318 Cov.: 32 AF XY: 0.573 AC XY: 42621 AN XY: 74384

Gnomad4 AFR AF: 0.736

Gnomad4 AMR AF: 0.459

Gnomad4 ASJ AF: 0.583

Gnomad4 EAS AF: 0.633

Gnomad4 SAS AF: 0.457

Gnomad4 FIN AF: 0.511

Gnomad4 NFE AF: 0.526

Gnomad4 OTH AF: 0.569

Alfa AF: 0.532 Hom.: 10953

Bravo AF: 0.582

Asia WGS AF: 0.564 AC: 1963 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.49
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs337663; hg19: chr12-92705204;