rs1440853

Variant names:

• chr4-79585493-A-C
• rs1440853
• ENST00000661529.2:n.1165A>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 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=-0.91).
• 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 rank	MANE	Protein	UniProt
LOC107986294	XR_007058155.1	n.227+266A>C		intron_variant	Intron 2 of 6
LOC107986294	XR_007058156.1	n.491+266A>C		intron_variant	Intron 2 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00989	ENST00000661529.2	n.1165A>C		non_coding_transcript_exon_variant	Exon 4 of 4
LINC00989	ENST00000661950.1	n.1061A>C		non_coding_transcript_exon_variant	Exon 4 of 4
LINC00989	ENST00000767432.1	n.825A>C		non_coding_transcript_exon_variant	Exon 3 of 3

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

African (AFR) AF: 0.886 AC: 36802 AN: 41528

American (AMR) AF: 0.794 AC: 12135 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.845 AC: 2931 AN: 3470

East Asian (EAS) AF: 0.566 AC: 2908 AN: 5136

South Asian (SAS) AF: 0.481 AC: 2322 AN: 4824

European-Finnish (FIN) AF: 0.758 AC: 8024 AN: 10586

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

European-Non Finnish (NFE) AF: 0.796 AC: 54133 AN: 68000

Other (OTH) AF: 0.800 AC: 1686 AN: 2108

Alfa AF: 0.801 Hom.: 60868

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
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs1440853; hg19: chr4-80506647;