chr10-8930055-G-A

Variant names:

• chr10-8930055-G-A
• rs10508372
• ENST00000837048.1:n.752-212G>A

Variant summary

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

The ENST00000837048.1(LINC02676):​n.752-212G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.148 in 152,064 control chromosomes in the GnomAD database, including 2,752 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 0.15 (2752 hom., cov: 32)
• Consequence: LINC02676 ENST00000837048.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.19
• Publications: 40 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=-1.07).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.604 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000837048.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02676	ENST00000837048.1		n.752-212G>A		intron	N/A
	LINC02676	ENST00000837049.1		n.716-14043G>A		intron	N/A
	LINC02676	ENST00000837050.1		n.704-36488G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.147 AC: 22382 AN: 151946 Hom.: 2742 Cov.: 32

Gnomad AFR AF: 0.196

Gnomad AMI AF: 0.0418

Gnomad AMR AF: 0.218

Gnomad ASJ AF: 0.181

Gnomad EAS AF: 0.622

Gnomad SAS AF: 0.270

Gnomad FIN AF: 0.0604

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.0697

Gnomad OTH AF: 0.159

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

GnomAD4 genome AF: 0.148 AC: 22432 AN: 152064 Hom.: 2752 Cov.: 32 AF XY: 0.154 AC XY: 11473 AN XY: 74334

African (AFR) AF: 0.196 AC: 8123 AN: 41450

American (AMR) AF: 0.218 AC: 3339 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.181 AC: 627 AN: 3466

East Asian (EAS) AF: 0.622 AC: 3204 AN: 5150

South Asian (SAS) AF: 0.270 AC: 1300 AN: 4806

European-Finnish (FIN) AF: 0.0604 AC: 640 AN: 10598

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.0697 AC: 4741 AN: 67998

Other (OTH) AF: 0.166 AC: 349 AN: 2108

Alfa AF: 0.101 Hom.: 5530

Bravo AF: 0.161

Asia WGS AF: 0.433 AC: 1505 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.20
DANN	Benign	0.77
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs10508372; hg19: chr10-8972018;