rs3899823

Positions:

• chr6-31442820-G-A

Variant summary

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

The NR_144465.1(LINC01149):​n.645+509G>A 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 0.275 in 151,548 control chromosomes in the GnomAD database, including 6,602 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 0.27 (6602 hom., cov: 31)
• Consequence: LINC01149 NR_144465.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.137

Genes affected

LINC01149 (HGNC:39757): (long intergenic non-protein coding RNA 1149)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.394 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01149	NR_144465.1	n.645+509G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01149	ENST00000430364.1	n.645+509G>A		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.274 AC: 41566 AN: 151430 Hom.: 6598 Cov.: 31

Gnomad AFR AF: 0.399

Gnomad AMI AF: 0.353

Gnomad AMR AF: 0.335

Gnomad ASJ AF: 0.325

Gnomad EAS AF: 0.194

Gnomad SAS AF: 0.263

Gnomad FIN AF: 0.267

Gnomad MID AF: 0.396

Gnomad NFE AF: 0.189

Gnomad OTH AF: 0.286

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

GnomAD4 genome AF: 0.275 AC: 41614 AN: 151548 Hom.: 6602 Cov.: 31 AF XY: 0.279 AC XY: 20696 AN XY: 74056

Gnomad4 AFR AF: 0.399

Gnomad4 AMR AF: 0.335

Gnomad4 ASJ AF: 0.325

Gnomad4 EAS AF: 0.194

Gnomad4 SAS AF: 0.262

Gnomad4 FIN AF: 0.267

Gnomad4 NFE AF: 0.189

Gnomad4 OTH AF: 0.282

Alfa AF: 0.236 Hom.: 1611

Bravo AF: 0.285

Asia WGS AF: 0.267 AC: 927 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	7.1
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3899823; hg19: chr6-31410597;