rs12567209

chr1-162066689-G-Achr1-162066689-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 0.0888 in 152,094 control chromosomes in the GnomAD database, including 737 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 0.089 (737 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.19

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.205 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: 0.0888 AC: 13503 AN: 151976 Hom.: 738 Cov.: 32

Gnomad AFR AF: 0.0737

Gnomad AMI AF: 0.0833

Gnomad AMR AF: 0.119

Gnomad ASJ AF: 0.0770

Gnomad EAS AF: 0.166

Gnomad SAS AF: 0.217

Gnomad FIN AF: 0.107

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0740

Gnomad OTH AF: 0.0917

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

GnomAD4 genome AF: 0.0888 AC: 13509 AN: 152094 Hom.: 737 Cov.: 32 AF XY: 0.0926 AC XY: 6882 AN XY: 74344

Gnomad4 AFR AF: 0.0739

Gnomad4 AMR AF: 0.119

Gnomad4 ASJ AF: 0.0770

Gnomad4 EAS AF: 0.166

Gnomad4 SAS AF: 0.216

Gnomad4 FIN AF: 0.107

Gnomad4 NFE AF: 0.0740

Gnomad4 OTH AF: 0.0917

Alfa AF: 0.0752 Hom.: 655

Bravo AF: 0.0857

Asia WGS AF: 0.186 AC: 643 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	5.5
Dann	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12567209; hg19: chr1-162036479;