rs2878722

Variant names:

• chr18-42603653-G-A
• rs2878722
• ENST00000589068.5:n.1236+28462G>A

Variant summary

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

The ENST00000589068.5(LINC00907):​n.1236+28462G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.847 in 152,234 control chromosomes in the GnomAD database, including 55,143 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 0.85 (55143 hom., cov: 32)
• Consequence: LINC00907 ENST00000589068.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.108
• Publications: 4 publications found

Genes affected

LINC00907 (HGNC:44327): (long intergenic non-protein coding RNA 907)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.974 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000589068.5. 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
	LINC00907	NR_046174.2		n.1271+28462G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00907	ENST00000589068.5	TSL:2	n.1236+28462G>A		intron	N/A
	LINC00907	ENST00000753323.1		n.557-39266G>A		intron	N/A
	LINC00907	ENST00000753324.1		n.991+28462G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.846 AC: 128749 AN: 152114 Hom.: 55076 Cov.: 32

Gnomad AFR AF: 0.957

Gnomad AMI AF: 0.899

Gnomad AMR AF: 0.866

Gnomad ASJ AF: 0.792

Gnomad EAS AF: 0.996

Gnomad SAS AF: 0.855

Gnomad FIN AF: 0.816

Gnomad MID AF: 0.790

Gnomad NFE AF: 0.770

Gnomad OTH AF: 0.823

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

GnomAD4 genome AF: 0.847 AC: 128880 AN: 152234 Hom.: 55143 Cov.: 32 AF XY: 0.852 AC XY: 63424 AN XY: 74410

African (AFR) AF: 0.958 AC: 39812 AN: 41572

American (AMR) AF: 0.866 AC: 13250 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.792 AC: 2745 AN: 3466

East Asian (EAS) AF: 0.996 AC: 5139 AN: 5158

South Asian (SAS) AF: 0.855 AC: 4125 AN: 4826

European-Finnish (FIN) AF: 0.816 AC: 8652 AN: 10598

Middle Eastern (MID) AF: 0.803 AC: 236 AN: 294

European-Non Finnish (NFE) AF: 0.770 AC: 52357 AN: 67992

Other (OTH) AF: 0.824 AC: 1744 AN: 2116

Alfa AF: 0.820 Hom.: 42110

Bravo AF: 0.855

Asia WGS AF: 0.926 AC: 3218 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.8
DANN	Benign	0.37
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs2878722; hg19: chr18-40183618;