rs6708331

Variant names:

• chr2-70141791-G-A
• rs6708331
• ENST00000812224.1:n.512G>A

Variant summary

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

The ENST00000812224.1(ENSG00000305652):​n.512G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.244 in 152,146 control chromosomes in the GnomAD database, including 4,990 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 0.24 (4990 hom., cov: 33)
• Consequence: ENSG00000305652 ENST00000812224.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0150
• Publications: 14 publications found

Genes affected

ENSG00000305652 (HGNC:):

LINC01816 (HGNC:52621): (long intergenic non-protein coding RNA 1816)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.317 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
ENSG00000305652	ENST00000812224.1	n.512G>A		non_coding_transcript_exon_variant	Exon 1 of 1
LINC01816	ENST00000716052.1	n.125+878C>T		intron_variant	Intron 1 of 4
LINC01816	ENST00000716055.1	n.103+552C>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.244 AC: 37078 AN: 152028 Hom.: 4984 Cov.: 33

Gnomad AFR AF: 0.322

Gnomad AMI AF: 0.309

Gnomad AMR AF: 0.135

Gnomad ASJ AF: 0.103

Gnomad EAS AF: 0.112

Gnomad SAS AF: 0.0834

Gnomad FIN AF: 0.318

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.239

Gnomad OTH AF: 0.193

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

GnomAD4 genome AF: 0.244 AC: 37121 AN: 152146 Hom.: 4990 Cov.: 33 AF XY: 0.242 AC XY: 17974 AN XY: 74394

African (AFR) AF: 0.322 AC: 13361 AN: 41504

American (AMR) AF: 0.135 AC: 2061 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.103 AC: 357 AN: 3468

East Asian (EAS) AF: 0.112 AC: 582 AN: 5184

South Asian (SAS) AF: 0.0843 AC: 407 AN: 4828

European-Finnish (FIN) AF: 0.318 AC: 3366 AN: 10584

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.239 AC: 16273 AN: 67978

Other (OTH) AF: 0.192 AC: 406 AN: 2114

Alfa AF: 0.227 Hom.: 10616

Bravo AF: 0.234

Asia WGS AF: 0.128 AC: 442 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	2.5
DANN	Benign	0.51
PhyloP100		-0.015

Splicing

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

Other links and lift over

dbSNP: rs6708331; hg19: chr2-70368923;