12-57848762-T-G

Variant names:

• chr12-57848762-T-G
• rs1599750

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0480

ACMG classification

Verdict is Benign. Variant got -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

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

Gnomad4 AFR AF: 0.216

Gnomad4 AMR AF: 0.398

Gnomad4 ASJ AF: 0.219

Gnomad4 EAS AF: 0.742

Gnomad4 SAS AF: 0.592

Gnomad4 FIN AF: 0.408

Gnomad4 NFE AF: 0.309

Gnomad4 OTH AF: 0.292

Alfa AF: 0.304 Hom.: 11383

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1599750; hg19: chr12-58242545;