rs9574309

Positions:

• chr13-78807966-T-C

Variant summary

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

The NR_046869.2(LINC00331):​n.225-15664A>G 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 0.45 in 151,692 control chromosomes in the GnomAD database, including 15,661 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 0.45 (15661 hom., cov: 32)
• Consequence: LINC00331 NR_046869.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.980

Genes affected

LINC00331 (HGNC:42048): (long intergenic non-protein coding RNA 331)

ACMG classification

Verdict is Benign. Variant got -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 = 0.502 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC00331	NR_046869.2	n.225-15664A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00331	ENST00000667185.1	n.225+16778A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.450 AC: 68140 AN: 151574 Hom.: 15638 Cov.: 32

Gnomad AFR AF: 0.508

Gnomad AMI AF: 0.326

Gnomad AMR AF: 0.507

Gnomad ASJ AF: 0.458

Gnomad EAS AF: 0.462

Gnomad SAS AF: 0.387

Gnomad FIN AF: 0.378

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.417

Gnomad OTH AF: 0.454

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

GnomAD4 genome AF: 0.450 AC: 68199 AN: 151692 Hom.: 15661 Cov.: 32 AF XY: 0.449 AC XY: 33265 AN XY: 74140

Gnomad4 AFR AF: 0.508

Gnomad4 AMR AF: 0.507

Gnomad4 ASJ AF: 0.458

Gnomad4 EAS AF: 0.461

Gnomad4 SAS AF: 0.386

Gnomad4 FIN AF: 0.378

Gnomad4 NFE AF: 0.417

Gnomad4 OTH AF: 0.456

Alfa AF: 0.427 Hom.: 24376

Bravo AF: 0.464

Asia WGS AF: 0.456 AC: 1580 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.5
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9574309; hg19: chr13-79382101;