13-89206246-A-G

Position:

• chr13-89206246-A-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, non coding transcript 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, non_coding_transcript
• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00440	ENST00000653072.1	n.28+24895A>G		intron_variant, non_coding_transcript_variant

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;