rs12160908

chr22-25532653-C-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 0.119 in 151,878 control chromosomes in the GnomAD database, including 1,124 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 0.12 (1124 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.46

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.127 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: 0.119 AC: 18027 AN: 151762 Hom.: 1120 Cov.: 31

Gnomad AFR AF: 0.117

Gnomad AMI AF: 0.0208

Gnomad AMR AF: 0.118

Gnomad ASJ AF: 0.136

Gnomad EAS AF: 0.00270

Gnomad SAS AF: 0.0984

Gnomad FIN AF: 0.128

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.129

Gnomad OTH AF: 0.116

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

GnomAD4 genome AF: 0.119 AC: 18052 AN: 151878 Hom.: 1124 Cov.: 31 AF XY: 0.118 AC XY: 8727 AN XY: 74260

Gnomad4 AFR AF: 0.118

Gnomad4 AMR AF: 0.118

Gnomad4 ASJ AF: 0.136

Gnomad4 EAS AF: 0.00271

Gnomad4 SAS AF: 0.0985

Gnomad4 FIN AF: 0.128

Gnomad4 NFE AF: 0.129

Gnomad4 OTH AF: 0.115

Alfa AF: 0.127 Hom.: 1465

Bravo AF: 0.117

Asia WGS AF: 0.0490 AC: 168 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.19
Dann	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12160908; hg19: chr22-25928620;