ENST00000626474.3:n.358+8303A>G

Variant names:

• chr3-72266805-T-C
• rs4532099
• ENST00000626474.3:n.358+8303A>G

Variant summary

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

The ENST00000626474.3(LINC00877):​n.358+8303A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.814 in 149,218 control chromosomes in the GnomAD database, including 49,847 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 0.81 (49847 hom., cov: 25)
• Consequence: LINC00877 ENST00000626474.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.44
• Publications: 8 publications found

Genes affected

LINC00877 (HGNC:27706): (long intergenic non-protein coding RNA 877)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.913 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000626474.3. 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
	LINC00877	ENST00000626474.3	TSL:5	n.358+8303A>G		intron	N/A
	LINC00877	ENST00000664517.1		n.169+8303A>G		intron	N/A
	LINC00877	ENST00000690747.1		n.103+8303A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.814 AC: 121437 AN: 149102 Hom.: 49804 Cov.: 25

Gnomad AFR AF: 0.920

Gnomad AMI AF: 0.796

Gnomad AMR AF: 0.783

Gnomad ASJ AF: 0.726

Gnomad EAS AF: 0.847

Gnomad SAS AF: 0.744

Gnomad FIN AF: 0.828

Gnomad MID AF: 0.735

Gnomad NFE AF: 0.765

Gnomad OTH AF: 0.794

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

GnomAD4 genome AF: 0.814 AC: 121537 AN: 149218 Hom.: 49847 Cov.: 25 AF XY: 0.816 AC XY: 59264 AN XY: 72596

African (AFR) AF: 0.920 AC: 37082 AN: 40286

American (AMR) AF: 0.783 AC: 11715 AN: 14964

Ashkenazi Jewish (ASJ) AF: 0.726 AC: 2511 AN: 3460

East Asian (EAS) AF: 0.846 AC: 4244 AN: 5014

South Asian (SAS) AF: 0.742 AC: 3467 AN: 4672

European-Finnish (FIN) AF: 0.828 AC: 8330 AN: 10056

Middle Eastern (MID) AF: 0.740 AC: 213 AN: 288

European-Non Finnish (NFE) AF: 0.765 AC: 51603 AN: 67498

Other (OTH) AF: 0.796 AC: 1648 AN: 2070

Alfa AF: 0.776 Hom.: 204638

Bravo AF: 0.816

Asia WGS AF: 0.791 AC: 2695 AN: 3406

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.44
DANN	Benign	0.34
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs4532099; hg19: chr3-72315956;