rs9307551

Positions:

• chr4-79609517-A-C
• chr4-79609517-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000668018.1(LINC00989):​n.673+2561A>C variant causes a intron, non coding transcript 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.347

Genes affected

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

LOC107986294 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LOC107986294	XR_007058155.1	n.632+2557A>C		intron_variant, non_coding_transcript_variant
LOC107986294	XR_007058156.1	n.896+2557A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00989	ENST00000668018.1	n.673+2561A>C		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.779

Gnomad4 AMR AF: 0.798

Gnomad4 ASJ AF: 0.847

Gnomad4 EAS AF: 0.569

Gnomad4 SAS AF: 0.482

Gnomad4 FIN AF: 0.775

Gnomad4 NFE AF: 0.798

Gnomad4 OTH AF: 0.791

Alfa AF: 0.794 Hom.: 5976

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9307551; hg19: chr4-80530671;