chr12-38269094-C-T

Variant names:

• chr12-38269094-C-T
• rs1963562

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 0.301 in 152,074 control chromosomes in the GnomAD database, including 8,897 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 0.30 (8897 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.189

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.427 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: 0.301 AC: 45766 AN: 151956 Hom.: 8895 Cov.: 32

Gnomad AFR AF: 0.0886

Gnomad AMI AF: 0.370

Gnomad AMR AF: 0.279

Gnomad ASJ AF: 0.295

Gnomad EAS AF: 0.0311

Gnomad SAS AF: 0.262

Gnomad FIN AF: 0.478

Gnomad MID AF: 0.357

Gnomad NFE AF: 0.431

Gnomad OTH AF: 0.289

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

GnomAD4 genome AF: 0.301 AC: 45760 AN: 152074 Hom.: 8897 Cov.: 32 AF XY: 0.300 AC XY: 22261 AN XY: 74320

Gnomad4 AFR AF: 0.0883

Gnomad4 AMR AF: 0.279

Gnomad4 ASJ AF: 0.295

Gnomad4 EAS AF: 0.0310

Gnomad4 SAS AF: 0.263

Gnomad4 FIN AF: 0.478

Gnomad4 NFE AF: 0.431

Gnomad4 OTH AF: 0.285

Alfa AF: 0.382 Hom.: 3218

Bravo AF: 0.279

Asia WGS AF: 0.145 AC: 508 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.9
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1963562; hg19: chr12-38662896;