12-57848762-T-G

Variant names:

• chr12-57848762-T-G
• rs1599750
• ENST00000724386.1:n.216+2383T>G

Variant summary

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

The ENST00000724386.1(ENSG00000294563):​n.216+2383T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.32 in 151,910 control chromosomes in the GnomAD database, including 8,894 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 0.32 (8894 hom., cov: 31)
• Consequence: ENSG00000294563 ENST00000724386.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0480
• Publications: 16 publications found

Genes affected

ENSG00000294563 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.723 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
ENSG00000294563	ENST00000724386.1	n.216+2383T>G		intron_variant	Intron 1 of 1
ENSG00000294563	ENST00000724391.1	n.216+2383T>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.320 AC: 48602 AN: 151792 Hom.: 8865 Cov.: 31

Gnomad AFR AF: 0.215

Gnomad AMI AF: 0.299

Gnomad AMR AF: 0.397

Gnomad ASJ AF: 0.219

Gnomad EAS AF: 0.742

Gnomad SAS AF: 0.591

Gnomad FIN AF: 0.408

Gnomad MID AF: 0.121

Gnomad NFE AF: 0.309

Gnomad OTH AF: 0.285

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

GnomAD4 genome AF: 0.320 AC: 48678 AN: 151910 Hom.: 8894 Cov.: 31 AF XY: 0.332 AC XY: 24649 AN XY: 74236

African (AFR) AF: 0.216 AC: 8927 AN: 41412

American (AMR) AF: 0.398 AC: 6082 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.219 AC: 761 AN: 3468

East Asian (EAS) AF: 0.742 AC: 3827 AN: 5156

South Asian (SAS) AF: 0.592 AC: 2849 AN: 4814

European-Finnish (FIN) AF: 0.408 AC: 4307 AN: 10550

Middle Eastern (MID) AF: 0.123 AC: 36 AN: 292

European-Non Finnish (NFE) AF: 0.309 AC: 21002 AN: 67928

Other (OTH) AF: 0.292 AC: 615 AN: 2108

Alfa AF: 0.306 Hom.: 17790

Bravo AF: 0.315

Asia WGS AF: 0.636 AC: 2208 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	5.2
DANN	Benign	0.44
PhyloP100		-0.048

Splicing

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

Other links and lift over

dbSNP: rs1599750; hg19: chr12-58242545;