ENST00000668018.1:n.673+2561A>C

Variant names:

• chr4-79609517-A-C
• rs9307551
• ENST00000668018.1:n.673+2561A>C

Variant summary

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

The ENST00000668018.1(LINC00989):​n.673+2561A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.78 (41180 hom., cov: 17)
• Consequence: LINC00989 ENST00000668018.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.347
• Publications: 21 publications found

Genes affected

LINC00989 (HGNC:48918): (long intergenic non-protein coding RNA 989)

LOC107986294 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.793 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107986294	XR_007058155.1	n.632+2557A>C		intron_variant	Intron 6 of 6
LOC107986294	XR_007058156.1	n.896+2557A>C		intron_variant	Intron 6 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00989	ENST00000668018.1	n.673+2561A>C		intron_variant	Intron 4 of 4
LINC00989	ENST00000767419.1	n.1027+2561A>C		intron_variant	Intron 6 of 6
LINC00989	ENST00000767420.1	n.1018+2561A>C		intron_variant	Intron 6 of 6

Frequencies

GnomAD3 genomes AF: 0.776 AC: 105804 AN: 136326 Hom.: 41154 Cov.: 17

Gnomad AFR AF: 0.779

Gnomad AMI AF: 0.828

Gnomad AMR AF: 0.798

Gnomad ASJ AF: 0.847

Gnomad EAS AF: 0.568

Gnomad SAS AF: 0.483

Gnomad FIN AF: 0.775

Gnomad MID AF: 0.802

Gnomad NFE AF: 0.798

Gnomad OTH AF: 0.792

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

GnomAD4 genome AF: 0.776 AC: 105866 AN: 136398 Hom.: 41180 Cov.: 17 AF XY: 0.770 AC XY: 50178 AN XY: 65158

African (AFR) AF: 0.779 AC: 28187 AN: 36206

American (AMR) AF: 0.798 AC: 10481 AN: 13136

Ashkenazi Jewish (ASJ) AF: 0.847 AC: 2879 AN: 3400

East Asian (EAS) AF: 0.569 AC: 2538 AN: 4464

South Asian (SAS) AF: 0.482 AC: 1982 AN: 4108

European-Finnish (FIN) AF: 0.775 AC: 5406 AN: 6972

Middle Eastern (MID) AF: 0.813 AC: 208 AN: 256

European-Non Finnish (NFE) AF: 0.798 AC: 51975 AN: 65104

Other (OTH) AF: 0.791 AC: 1486 AN: 1878

Alfa AF: 0.793 Hom.: 6211

Bravo AF: 0.778

Asia WGS AF: 0.557 AC: 1938 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.0
DANN	Benign	0.66
PhyloP100		0.35

Splicing

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

Other links and lift over

dbSNP: rs9307551; hg19: chr4-80530671;