rs7662551

Variant names:

• chr4-79616484-G-A
• rs7662551
• ENST00000668018.1:n.674-6744G>A

Variant summary

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

The ENST00000668018.1(LINC00989):​n.674-6744G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.772 in 151,934 control chromosomes in the GnomAD database, including 45,956 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 0.77 (45956 hom., cov: 31)
• Consequence: LINC00989 ENST00000668018.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.758
• Publications: 8 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=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.886 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000668018.1. 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
	LINC00989	ENST00000668018.1		n.674-6744G>A		intron	N/A
	LINC00989	ENST00000767419.1		n.1028-6744G>A		intron	N/A
	LINC00989	ENST00000767420.1		n.1019-6744G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.772 AC: 117168 AN: 151816 Hom.: 45911 Cov.: 31

Gnomad AFR AF: 0.894

Gnomad AMI AF: 0.810

Gnomad AMR AF: 0.707

Gnomad ASJ AF: 0.816

Gnomad EAS AF: 0.627

Gnomad SAS AF: 0.473

Gnomad FIN AF: 0.726

Gnomad MID AF: 0.766

Gnomad NFE AF: 0.748

Gnomad OTH AF: 0.772

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

GnomAD4 genome AF: 0.772 AC: 117267 AN: 151934 Hom.: 45956 Cov.: 31 AF XY: 0.765 AC XY: 56836 AN XY: 74250

African (AFR) AF: 0.894 AC: 37078 AN: 41472

American (AMR) AF: 0.707 AC: 10773 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.816 AC: 2829 AN: 3468

East Asian (EAS) AF: 0.627 AC: 3221 AN: 5136

South Asian (SAS) AF: 0.472 AC: 2269 AN: 4812

European-Finnish (FIN) AF: 0.726 AC: 7673 AN: 10564

Middle Eastern (MID) AF: 0.786 AC: 231 AN: 294

European-Non Finnish (NFE) AF: 0.748 AC: 50826 AN: 67928

Other (OTH) AF: 0.772 AC: 1628 AN: 2110

Alfa AF: 0.761 Hom.: 7244

Bravo AF: 0.780

Asia WGS AF: 0.573 AC: 1994 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.3
DANN	Benign	0.44
PhyloP100		0.76

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs7662551;

hg19: chr4-80537638;