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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107986294	XR_007058155.1	n.633-6744G>A		intron_variant	Intron 6 of 6
LOC107986294	XR_007058156.1	n.897-6744G>A		intron_variant	Intron 6 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00989	ENST00000668018.1	n.674-6744G>A		intron_variant	Intron 4 of 4
LINC00989	ENST00000767419.1	n.1028-6744G>A		intron_variant	Intron 6 of 6
LINC00989	ENST00000767420.1	n.1019-6744G>A		intron_variant	Intron 6 of 6

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 v4.3

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

Other links and lift over

dbSNP: rs7662551; hg19: chr4-80537638;