10-8912261-A-G

Variant names:

• chr10-8912261-A-G
• rs2388896
• ENST00000447297.1:n.176-1561A>G

Variant summary

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

The ENST00000447297.1(LINC02676):​n.176-1561A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.64 in 151,896 control chromosomes in the GnomAD database, including 31,519 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 0.64 (31519 hom., cov: 32)
• Consequence: LINC02676 ENST00000447297.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.137
• Publications: 12 publications found

Genes affected

LINC02676 (HGNC:54170): (long intergenic non-protein coding RNA 2676)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.812 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02676	NR_131944.1	n.176-1561A>G		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02676	ENST00000447297.1	n.176-1561A>G		intron_variant	Intron 2 of 3	3
LINC02676	ENST00000837048.1	n.752-18006A>G		intron_variant	Intron 1 of 4
LINC02676	ENST00000837049.1	n.716-31837A>G		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.640 AC: 97082 AN: 151776 Hom.: 31485 Cov.: 32

Gnomad AFR AF: 0.603

Gnomad AMI AF: 0.734

Gnomad AMR AF: 0.751

Gnomad ASJ AF: 0.591

Gnomad EAS AF: 0.833

Gnomad SAS AF: 0.691

Gnomad FIN AF: 0.633

Gnomad MID AF: 0.603

Gnomad NFE AF: 0.621

Gnomad OTH AF: 0.633

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

GnomAD4 genome AF: 0.640 AC: 97159 AN: 151896 Hom.: 31519 Cov.: 32 AF XY: 0.644 AC XY: 47802 AN XY: 74216

African (AFR) AF: 0.602 AC: 24949 AN: 41426

American (AMR) AF: 0.752 AC: 11456 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.591 AC: 2049 AN: 3468

East Asian (EAS) AF: 0.832 AC: 4290 AN: 5154

South Asian (SAS) AF: 0.693 AC: 3337 AN: 4814

European-Finnish (FIN) AF: 0.633 AC: 6664 AN: 10524

Middle Eastern (MID) AF: 0.610 AC: 178 AN: 292

European-Non Finnish (NFE) AF: 0.621 AC: 42223 AN: 67960

Other (OTH) AF: 0.637 AC: 1345 AN: 2110

Alfa AF: 0.628 Hom.: 50887

Bravo AF: 0.646

Asia WGS AF: 0.764 AC: 2657 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.3
DANN	Benign	0.59
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs2388896; hg19: chr10-8954224;