rs3899823

Variant names:

• chr6-31442820-G-A
• rs3899823
• ENST00000430364.1:n.645+509G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000430364.1(LINC01149):​n.645+509G>A variant causes a intron 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 ENST00000430364.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.137
• Publications: 9 publications found

Genes affected

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

ENSG00000288587 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LINC01149	NR_144465.1	n.645+509G>A		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01149	ENST00000430364.1	n.645+509G>A		intron_variant	Intron 1 of 1	1
ENSG00000288587	ENST00000673857.1	n.63-20303G>A		intron_variant	Intron 1 of 2
LINC01149	ENST00000812003.1	n.669+509G>A		intron_variant	Intron 1 of 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

African (AFR) AF: 0.399 AC: 16431 AN: 41172

American (AMR) AF: 0.335 AC: 5080 AN: 15168

Ashkenazi Jewish (ASJ) AF: 0.325 AC: 1126 AN: 3466

East Asian (EAS) AF: 0.194 AC: 1002 AN: 5152

South Asian (SAS) AF: 0.262 AC: 1257 AN: 4798

European-Finnish (FIN) AF: 0.267 AC: 2818 AN: 10538

Middle Eastern (MID) AF: 0.398 AC: 117 AN: 294

European-Non Finnish (NFE) AF: 0.189 AC: 12868 AN: 67944

Other (OTH) AF: 0.282 AC: 594 AN: 2106

Alfa AF: 0.237 Hom.: 2312

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
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs3899823; hg19: chr6-31410597;