10-8912261-A-G

Position:

• chr10-8912261-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_131944.1(LINC02676):​n.176-1561A>G variant causes a intron, non coding transcript 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 NR_131944.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.137

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
LINC02676	NR_131944.1	n.176-1561A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02676	ENST00000447297.1	n.176-1561A>G		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.602

Gnomad4 AMR AF: 0.752

Gnomad4 ASJ AF: 0.591

Gnomad4 EAS AF: 0.832

Gnomad4 SAS AF: 0.693

Gnomad4 FIN AF: 0.633

Gnomad4 NFE AF: 0.621

Gnomad4 OTH AF: 0.637

Alfa AF: 0.628 Hom.: 13944

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2388896; hg19: chr10-8954224;