chr12-33996498-G-T

Position:

• chr12-33996498-G-T

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 0.255 in 151,732 control chromosomes in the GnomAD database, including 5,534 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 0.26 (5534 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.485

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.378 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.255 AC: 38670 AN: 151616 Hom.: 5524 Cov.: 31

Gnomad AFR AF: 0.383

Gnomad AMI AF: 0.325

Gnomad AMR AF: 0.206

Gnomad ASJ AF: 0.220

Gnomad EAS AF: 0.127

Gnomad SAS AF: 0.126

Gnomad FIN AF: 0.201

Gnomad MID AF: 0.194

Gnomad NFE AF: 0.217

Gnomad OTH AF: 0.233

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

GnomAD4 genome AF: 0.255 AC: 38717 AN: 151732 Hom.: 5534 Cov.: 31 AF XY: 0.252 AC XY: 18681 AN XY: 74142

Gnomad4 AFR AF: 0.383

Gnomad4 AMR AF: 0.206

Gnomad4 ASJ AF: 0.220

Gnomad4 EAS AF: 0.127

Gnomad4 SAS AF: 0.126

Gnomad4 FIN AF: 0.201

Gnomad4 NFE AF: 0.217

Gnomad4 OTH AF: 0.231

Alfa AF: 0.217 Hom.: 4831

Bravo AF: 0.262

Asia WGS AF: 0.154 AC: 534 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.38
DANN	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1627770; hg19: chr12-34149433;