ENST00000834589.1:n.142-309C>T

Variant names:

• chr12-25331259-C-T
• rs7965364
• ENST00000834589.1:n.142-309C>T

Variant summary

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

The ENST00000834589.1(ENSG00000308495):​n.142-309C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.705 in 152,128 control chromosomes in the GnomAD database, including 41,396 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 0.70 (41396 hom., cov: 32)
• Consequence: ENSG00000308495 ENST00000834589.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.31
• Publications: 4 publications found

Genes affected

ENSG00000308495 (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 (NFE) allele frequency at 95% confidence interval = 0.855 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
ENSG00000308495	ENST00000834589.1	n.142-309C>T		intron_variant	Intron 1 of 2
ENSG00000308495	ENST00000834590.1	n.142-309C>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.705 AC: 107185 AN: 152010 Hom.: 41405 Cov.: 32

Gnomad AFR AF: 0.361

Gnomad AMI AF: 0.952

Gnomad AMR AF: 0.761

Gnomad ASJ AF: 0.805

Gnomad EAS AF: 0.756

Gnomad SAS AF: 0.675

Gnomad FIN AF: 0.895

Gnomad MID AF: 0.753

Gnomad NFE AF: 0.861

Gnomad OTH AF: 0.728

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

GnomAD4 genome AF: 0.705 AC: 107185 AN: 152128 Hom.: 41396 Cov.: 32 AF XY: 0.705 AC XY: 52454 AN XY: 74386

African (AFR) AF: 0.360 AC: 14929 AN: 41438

American (AMR) AF: 0.761 AC: 11630 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.805 AC: 2796 AN: 3472

East Asian (EAS) AF: 0.756 AC: 3907 AN: 5168

South Asian (SAS) AF: 0.674 AC: 3255 AN: 4826

European-Finnish (FIN) AF: 0.895 AC: 9498 AN: 10610

Middle Eastern (MID) AF: 0.759 AC: 223 AN: 294

European-Non Finnish (NFE) AF: 0.861 AC: 58550 AN: 68016

Other (OTH) AF: 0.725 AC: 1531 AN: 2112

Alfa AF: 0.782 Hom.: 78549

Bravo AF: 0.681

Asia WGS AF: 0.651 AC: 2266 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.48
DANN	Benign	0.56
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs7965364; hg19: chr12-25484193;