12-58407244-C-T

Variant names:

• chr12-58407244-C-T
• rs3842936
• ENST00000841855.1:n.68+615C>T

Variant summary

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

The ENST00000841855.1(ENSG00000309533):​n.68+615C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.445 in 151,564 control chromosomes in the GnomAD database, including 15,179 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 0.45 (15179 hom., cov: 30)
• Consequence: ENSG00000309533 ENST00000841855.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08
• Publications: 6 publications found

Genes affected

ENSG00000309533 (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 (SAS) allele frequency at 95% confidence interval = 0.497 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
ENSG00000309533	ENST00000841855.1	n.68+615C>T		intron_variant	Intron 1 of 1
ENSG00000309533	ENST00000841856.1	n.119+410C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.445 AC: 67460 AN: 151448 Hom.: 15170 Cov.: 30

Gnomad AFR AF: 0.469

Gnomad AMI AF: 0.394

Gnomad AMR AF: 0.346

Gnomad ASJ AF: 0.471

Gnomad EAS AF: 0.509

Gnomad SAS AF: 0.514

Gnomad FIN AF: 0.501

Gnomad MID AF: 0.379

Gnomad NFE AF: 0.435

Gnomad OTH AF: 0.436

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

GnomAD4 genome AF: 0.445 AC: 67492 AN: 151564 Hom.: 15179 Cov.: 30 AF XY: 0.447 AC XY: 33082 AN XY: 74036

African (AFR) AF: 0.469 AC: 19374 AN: 41278

American (AMR) AF: 0.345 AC: 5251 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.471 AC: 1635 AN: 3472

East Asian (EAS) AF: 0.507 AC: 2607 AN: 5140

South Asian (SAS) AF: 0.514 AC: 2471 AN: 4810

European-Finnish (FIN) AF: 0.501 AC: 5242 AN: 10462

Middle Eastern (MID) AF: 0.390 AC: 113 AN: 290

European-Non Finnish (NFE) AF: 0.435 AC: 29534 AN: 67874

Other (OTH) AF: 0.430 AC: 906 AN: 2106

Alfa AF: 0.435 Hom.: 49680

Bravo AF: 0.434

Asia WGS AF: 0.481 AC: 1677 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	1.7
DANN	Benign	0.44
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs3842936; hg19: chr12-58801027;