chr3-182251564-G-A

Variant names:

• chr3-182251564-G-A
• rs6791663
• ENST00000715740.1:n.880-34592C>T

Variant summary

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

The ENST00000715740.1(LINC01994):​n.880-34592C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.205 in 151,754 control chromosomes in the GnomAD database, including 3,728 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 0.20 (3728 hom., cov: 31)
• Consequence: LINC01994 ENST00000715740.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.686
• Publications: 2 publications found

Genes affected

LINC01994 (HGNC:52827): (long intergenic non-protein coding RNA 1994)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.353 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
LINC01994	ENST00000715740.1	n.880-34592C>T		intron_variant	Intron 6 of 7
LINC01994	ENST00000767325.1	n.201-16550C>T		intron_variant	Intron 2 of 3
LINC01994	ENST00000767326.1	n.318-34592C>T		intron_variant	Intron 3 of 4
LINC01994	ENST00000767329.1	n.196-34592C>T		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.205 AC: 31065 AN: 151636 Hom.: 3716 Cov.: 31

Gnomad AFR AF: 0.312

Gnomad AMI AF: 0.0680

Gnomad AMR AF: 0.145

Gnomad ASJ AF: 0.162

Gnomad EAS AF: 0.367

Gnomad SAS AF: 0.188

Gnomad FIN AF: 0.0800

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.165

Gnomad OTH AF: 0.207

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

GnomAD4 genome AF: 0.205 AC: 31103 AN: 151754 Hom.: 3728 Cov.: 31 AF XY: 0.201 AC XY: 14883 AN XY: 74166

African (AFR) AF: 0.312 AC: 12930 AN: 41378

American (AMR) AF: 0.145 AC: 2213 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.162 AC: 562 AN: 3466

East Asian (EAS) AF: 0.367 AC: 1885 AN: 5138

South Asian (SAS) AF: 0.187 AC: 899 AN: 4810

European-Finnish (FIN) AF: 0.0800 AC: 839 AN: 10490

Middle Eastern (MID) AF: 0.299 AC: 88 AN: 294

European-Non Finnish (NFE) AF: 0.165 AC: 11186 AN: 67878

Other (OTH) AF: 0.208 AC: 439 AN: 2114

Alfa AF: 0.175 Hom.: 1454

Bravo AF: 0.214

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.75
DANN	Benign	0.60
PhyloP100		-0.69

Splicing

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

Other links and lift over

dbSNP: rs6791663; hg19: chr3-181969352;