rs1440853

Positions:

• chr4-79585493-A-C

Variant summary

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

The ENST00000661529.2(LINC00989):​n.1165A>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.801 in 152,136 control chromosomes in the GnomAD database, including 49,471 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 (49471 hom., cov: 32)
• Consequence: LINC00989 ENST00000661529.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.70

Genes affected

LINC00989 (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 (AFR) allele frequency at 95% confidence interval = 0.879 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107986294	XR_007058155.1	n.227+266A>C		intron_variant
LOC107986294	XR_007058156.1	n.491+266A>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC00989	ENST00000661529.2	n.1165A>C		non_coding_transcript_exon_variant	4/4
LINC00989	ENST00000661950.1	n.1061A>C		non_coding_transcript_exon_variant	4/4
LINC00989	ENST00000668018.1	n.545+266A>C		intron_variant

Frequencies

GnomAD3 genomes AF: 0.801 AC: 121804 AN: 152016 Hom.: 49414 Cov.: 32

Gnomad AFR AF: 0.886

Gnomad AMI AF: 0.818

Gnomad AMR AF: 0.794

Gnomad ASJ AF: 0.845

Gnomad EAS AF: 0.566

Gnomad SAS AF: 0.482

Gnomad FIN AF: 0.758

Gnomad MID AF: 0.782

Gnomad NFE AF: 0.796

Gnomad OTH AF: 0.800

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

GnomAD4 genome AF: 0.801 AC: 121921 AN: 152136 Hom.: 49471 Cov.: 32 AF XY: 0.793 AC XY: 58937 AN XY: 74348

Gnomad4 AFR AF: 0.886

Gnomad4 AMR AF: 0.794

Gnomad4 ASJ AF: 0.845

Gnomad4 EAS AF: 0.566

Gnomad4 SAS AF: 0.481

Gnomad4 FIN AF: 0.758

Gnomad4 NFE AF: 0.796

Gnomad4 OTH AF: 0.800

Alfa AF: 0.796 Hom.: 45160

Bravo AF: 0.814

Asia WGS AF: 0.568 AC: 1976 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.47
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1440853; hg19: chr4-80506647;