rs12772023

Positions:

• chr10-106365433-C-T

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 0.0159 in 152,248 control chromosomes in the GnomAD database, including 24 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 0.016 (24 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.293

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0159 (2419/152248) while in subpopulation NFE AF= 0.02 (1359/68020). AF 95% confidence interval is 0.0191. There are 24 homozygotes in gnomad4. There are 1110 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 24 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: 0.0159 AC: 2419 AN: 152130 Hom.: 24 Cov.: 33

Gnomad AFR AF: 0.0123

Gnomad AMI AF: 0.00548

Gnomad AMR AF: 0.0109

Gnomad ASJ AF: 0.0560

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0153

Gnomad FIN AF: 0.00311

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.0200

Gnomad OTH AF: 0.0225

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

GnomAD4 genome AF: 0.0159 AC: 2419 AN: 152248 Hom.: 24 Cov.: 33 AF XY: 0.0149 AC XY: 1110 AN XY: 74426

Gnomad4 AFR AF: 0.0124

Gnomad4 AMR AF: 0.0108

Gnomad4 ASJ AF: 0.0560

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.0149

Gnomad4 FIN AF: 0.00311

Gnomad4 NFE AF: 0.0200

Gnomad4 OTH AF: 0.0227

Alfa AF: 0.0197 Hom.: 2

Bravo AF: 0.0168

Asia WGS AF: 0.00808 AC: 28 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	2.4
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12772023; hg19: chr10-108125191;