rs2336434

Variant names:

• chr12-65125486-T-G
• rs2336434

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 0.0309 in 152,184 control chromosomes in the GnomAD database, including 157 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 0.031 (157 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.21

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0799 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: 0.0309 AC: 4694 AN: 152066 Hom.: 155 Cov.: 32

Gnomad AFR AF: 0.0821

Gnomad AMI AF: 0.0219

Gnomad AMR AF: 0.0172

Gnomad ASJ AF: 0.0153

Gnomad EAS AF: 0.00173

Gnomad SAS AF: 0.0491

Gnomad FIN AF: 0.000849

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.00932

Gnomad OTH AF: 0.0301

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

GnomAD4 genome AF: 0.0309 AC: 4702 AN: 152184 Hom.: 157 Cov.: 32 AF XY: 0.0313 AC XY: 2332 AN XY: 74400

Gnomad4 AFR AF: 0.0822

Gnomad4 AMR AF: 0.0172

Gnomad4 ASJ AF: 0.0153

Gnomad4 EAS AF: 0.00174

Gnomad4 SAS AF: 0.0488

Gnomad4 FIN AF: 0.000849

Gnomad4 NFE AF: 0.00932

Gnomad4 OTH AF: 0.0298

Alfa AF: 0.0205 Hom.: 34

Bravo AF: 0.0328

Asia WGS AF: 0.0330 AC: 113 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.38
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2336434; hg19: chr12-65519266;