chr2-187978076-A-C

Variant names:

• chr2-187978076-A-C
• rs6713963
• ENST00000434418.2:n.496+57520T>G

Variant summary

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

The ENST00000434418.2(LINC01090):​n.496+57520T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.126 in 152,160 control chromosomes in the GnomAD database, including 1,315 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 0.13 (1315 hom., cov: 32)
• Consequence: LINC01090 ENST00000434418.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.38
• Publications: 4 publications found

Genes affected

LINC01090 (HGNC:49201): (long intergenic non-protein coding RNA 1090)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.158 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
LINC01090	ENST00000434418.2	n.496+57520T>G		intron_variant	Intron 3 of 3	5

Frequencies

GnomAD3 genomes AF: 0.126 AC: 19203 AN: 152042 Hom.: 1316 Cov.: 32

Gnomad AFR AF: 0.0915

Gnomad AMI AF: 0.147

Gnomad AMR AF: 0.0954

Gnomad ASJ AF: 0.138

Gnomad EAS AF: 0.00386

Gnomad SAS AF: 0.0803

Gnomad FIN AF: 0.162

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.161

Gnomad OTH AF: 0.127

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

GnomAD4 genome AF: 0.126 AC: 19209 AN: 152160 Hom.: 1315 Cov.: 32 AF XY: 0.124 AC XY: 9250 AN XY: 74392

African (AFR) AF: 0.0915 AC: 3801 AN: 41536

American (AMR) AF: 0.0951 AC: 1454 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.138 AC: 478 AN: 3464

East Asian (EAS) AF: 0.00387 AC: 20 AN: 5174

South Asian (SAS) AF: 0.0803 AC: 387 AN: 4818

European-Finnish (FIN) AF: 0.162 AC: 1710 AN: 10574

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.161 AC: 10915 AN: 67992

Other (OTH) AF: 0.128 AC: 269 AN: 2108

Alfa AF: 0.146 Hom.: 3559

Bravo AF: 0.121

Asia WGS AF: 0.0680 AC: 236 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	4.7
DANN	Benign	0.67
PhyloP100		2.4

Splicing

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

Other links and lift over

dbSNP: rs6713963; hg19: chr2-188842803;