13-89206246-A-G

Variant names:

• chr13-89206246-A-G
• rs2120871
• ENST00000653072.1:n.28+24895A>G

Variant summary

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

The ENST00000653072.1(LINC00440):​n.28+24895A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.758 in 152,030 control chromosomes in the GnomAD database, including 44,012 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 0.76 (44012 hom., cov: 32)
• Consequence: LINC00440 ENST00000653072.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.615

Genes affected

LINC00440 (HGNC:42777): (long intergenic non-protein coding RNA 440)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.799 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00440	ENST00000653072.1	n.28+24895A>G		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.758 AC: 115134 AN: 151912 Hom.: 43988 Cov.: 32

Gnomad AFR AF: 0.710

Gnomad AMI AF: 0.837

Gnomad AMR AF: 0.811

Gnomad ASJ AF: 0.796

Gnomad EAS AF: 0.623

Gnomad SAS AF: 0.792

Gnomad FIN AF: 0.642

Gnomad MID AF: 0.864

Gnomad NFE AF: 0.797

Gnomad OTH AF: 0.784

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

GnomAD4 genome AF: 0.758 AC: 115208 AN: 152030 Hom.: 44012 Cov.: 32 AF XY: 0.752 AC XY: 55844 AN XY: 74298

Gnomad4 AFR AF: 0.710

Gnomad4 AMR AF: 0.811

Gnomad4 ASJ AF: 0.796

Gnomad4 EAS AF: 0.623

Gnomad4 SAS AF: 0.791

Gnomad4 FIN AF: 0.642

Gnomad4 NFE AF: 0.797

Gnomad4 OTH AF: 0.783

Alfa AF: 0.794 Hom.: 59925

Bravo AF: 0.767

Asia WGS AF: 0.716 AC: 2492 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.0
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2120871; hg19: chr13-89858500;