4-79560662-T-C

Variant names:

• chr4-79560662-T-C
• rs1371993
• ENST00000508174.7:n.770-14479T>C

Variant summary

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

The ENST00000515544.2(LINC00989):​n.755-14479T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.796 in 151,950 control chromosomes in the GnomAD database, including 48,680 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 0.80 (48680 hom., cov: 30)
• Consequence: LINC00989 ENST00000515544.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.634
• Publications: 1 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.858 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000515544.2. 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
	LINC00989	NR_038826.1		n.735-14479T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00989	ENST00000508174.7	TSL:3	n.770-14479T>C		intron	N/A
	LINC00989	ENST00000515544.2	TSL:2	n.755-14479T>C		intron	N/A
	LINC00989	ENST00000661529.2		n.820-24486T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.796 AC: 120882 AN: 151832 Hom.: 48634 Cov.: 30

Gnomad AFR AF: 0.866

Gnomad AMI AF: 0.819

Gnomad AMR AF: 0.792

Gnomad ASJ AF: 0.844

Gnomad EAS AF: 0.568

Gnomad SAS AF: 0.482

Gnomad FIN AF: 0.761

Gnomad MID AF: 0.778

Gnomad NFE AF: 0.797

Gnomad OTH AF: 0.794

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

GnomAD4 genome AF: 0.796 AC: 120988 AN: 151950 Hom.: 48680 Cov.: 30 AF XY: 0.788 AC XY: 58533 AN XY: 74286

African (AFR) AF: 0.866 AC: 35911 AN: 41472

American (AMR) AF: 0.793 AC: 12105 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.844 AC: 2927 AN: 3466

East Asian (EAS) AF: 0.568 AC: 2917 AN: 5132

South Asian (SAS) AF: 0.481 AC: 2309 AN: 4796

European-Finnish (FIN) AF: 0.761 AC: 8032 AN: 10558

Middle Eastern (MID) AF: 0.796 AC: 234 AN: 294

European-Non Finnish (NFE) AF: 0.797 AC: 54129 AN: 67940

Other (OTH) AF: 0.795 AC: 1679 AN: 2112

Alfa AF: 0.807 Hom.: 6071

Bravo AF: 0.808

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.4
DANN	Benign	0.49
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs1371993; hg19: chr4-80481816;