6-31448379-A-G

Variant names:

• chr6-31448379-A-G
• rs2516464
• ENST00000673857.1:n.63-14744A>G

Variant summary

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

The ENST00000673857.1(ENSG00000288587):​n.63-14744A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.511 in 151,852 control chromosomes in the GnomAD database, including 20,615 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 0.51 (20615 hom., cov: 33)
• Consequence: ENSG00000288587 ENST00000673857.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.316
• Publications: 20 publications found

Genes affected

ENSG00000288587 (HGNC:):

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.58).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.56 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000288587	ENST00000673857.1	n.63-14744A>G		intron_variant	Intron 1 of 2
LINC01149	ENST00000812003.1	n.670-102A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.511 AC: 77544 AN: 151734 Hom.: 20581 Cov.: 33

Gnomad AFR AF: 0.565

Gnomad AMI AF: 0.640

Gnomad AMR AF: 0.546

Gnomad ASJ AF: 0.562

Gnomad EAS AF: 0.211

Gnomad SAS AF: 0.437

Gnomad FIN AF: 0.493

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.497

Gnomad OTH AF: 0.523

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

GnomAD4 genome AF: 0.511 AC: 77617 AN: 151852 Hom.: 20615 Cov.: 33 AF XY: 0.506 AC XY: 37551 AN XY: 74222

African (AFR) AF: 0.566 AC: 23370 AN: 41316

American (AMR) AF: 0.546 AC: 8313 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.562 AC: 1949 AN: 3466

East Asian (EAS) AF: 0.211 AC: 1093 AN: 5172

South Asian (SAS) AF: 0.439 AC: 2109 AN: 4806

European-Finnish (FIN) AF: 0.493 AC: 5198 AN: 10544

Middle Eastern (MID) AF: 0.466 AC: 136 AN: 292

European-Non Finnish (NFE) AF: 0.497 AC: 33773 AN: 67996

Other (OTH) AF: 0.517 AC: 1092 AN: 2112

Alfa AF: 0.502 Hom.: 45494

Bravo AF: 0.518

Asia WGS AF: 0.343 AC: 1191 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.58
CADD	Benign	13
DANN	Benign	0.96
PhyloP100		0.32

Splicing

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

Other links and lift over

dbSNP: rs2516464; hg19: chr6-31416156;