ENST00000789688.1:n.432-23998G>A

Variant names:

• chr12-5246207-G-A
• rs7302032
• ENST00000789688.1:n.432-23998G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000789688.1(ENSG00000256417):​n.432-23998G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0848 in 152,054 control chromosomes in the GnomAD database, including 724 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 0.085 (724 hom., cov: 32)
• Consequence: ENSG00000256417 ENST00000789688.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.604
• Publications: 1 publications found

Genes affected

ENSG00000256417 (HGNC:):

LINC02443 (HGNC:53375): (long intergenic non-protein coding RNA 2443)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.14 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105369617	NR_188065.1	n.772-23998G>A		intron_variant	Intron 4 of 10
LOC105369617	NR_188066.1	n.755-23998G>A		intron_variant	Intron 4 of 9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000256417	ENST00000789688.1	n.432-23998G>A		intron_variant	Intron 4 of 8
ENSG00000256417	ENST00000789689.1	n.503-23998G>A		intron_variant	Intron 5 of 11
ENSG00000256417	ENST00000789690.1	n.489-23998G>A		intron_variant	Intron 5 of 9

Frequencies

GnomAD3 genomes AF: 0.0847 AC: 12875 AN: 151936 Hom.: 722 Cov.: 32

Gnomad AFR AF: 0.143

Gnomad AMI AF: 0.120

Gnomad AMR AF: 0.0463

Gnomad ASJ AF: 0.118

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0564

Gnomad FIN AF: 0.0479

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0707

Gnomad OTH AF: 0.0687

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

GnomAD4 genome AF: 0.0848 AC: 12891 AN: 152054 Hom.: 724 Cov.: 32 AF XY: 0.0818 AC XY: 6080 AN XY: 74336

African (AFR) AF: 0.143 AC: 5923 AN: 41450

American (AMR) AF: 0.0460 AC: 703 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.118 AC: 408 AN: 3470

East Asian (EAS) AF: 0.000194 AC: 1 AN: 5164

South Asian (SAS) AF: 0.0565 AC: 271 AN: 4798

European-Finnish (FIN) AF: 0.0479 AC: 507 AN: 10580

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.0707 AC: 4809 AN: 67998

Other (OTH) AF: 0.0680 AC: 143 AN: 2104

Alfa AF: 0.0679 Hom.: 673

Bravo AF: 0.0875

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.75
DANN	Benign	0.67
PhyloP100		-0.60

Splicing

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

Other links and lift over

dbSNP: rs7302032; hg19: chr12-5355373;