chr12-53416668-A-G

Position:

• chr12-53416668-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0294 in 150,870 control chromosomes in the GnomAD database, including 98 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 0.029 (98 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.33

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0294 (4442/150870) while in subpopulation NFE AF= 0.0454 (3065/67524). AF 95% confidence interval is 0.0441. There are 98 homozygotes in gnomad4. There are 2145 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 98 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0295 AC: 4444 AN: 150752 Hom.: 98 Cov.: 31

Gnomad AFR AF: 0.00852

Gnomad AMI AF: 0.0241

Gnomad AMR AF: 0.0221

Gnomad ASJ AF: 0.0269

Gnomad EAS AF: 0.000386

Gnomad SAS AF: 0.0244

Gnomad FIN AF: 0.0384

Gnomad MID AF: 0.0224

Gnomad NFE AF: 0.0454

Gnomad OTH AF: 0.0248

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

GnomAD4 genome AF: 0.0294 AC: 4442 AN: 150870 Hom.: 98 Cov.: 31 AF XY: 0.0291 AC XY: 2145 AN XY: 73730

Gnomad4 AFR AF: 0.00850

Gnomad4 AMR AF: 0.0221

Gnomad4 ASJ AF: 0.0269

Gnomad4 EAS AF: 0.000387

Gnomad4 SAS AF: 0.0242

Gnomad4 FIN AF: 0.0384

Gnomad4 NFE AF: 0.0454

Gnomad4 OTH AF: 0.0245

Alfa AF: 0.0401 Hom.: 129

Bravo AF: 0.0267

Asia WGS AF: 0.0130 AC: 44 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.033
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: rs12821290; hg19: chr12-53810452;