rs12138969

chr1-207017819-G-A

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 0.14 in 152,206 control chromosomes in the GnomAD database, including 1,696 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 0.14 (1696 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0450

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.21 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: 0.140 AC: 21303 AN: 152088 Hom.: 1683 Cov.: 32

Gnomad AFR AF: 0.0817

Gnomad AMI AF: 0.0987

Gnomad AMR AF: 0.216

Gnomad ASJ AF: 0.227

Gnomad EAS AF: 0.0608

Gnomad SAS AF: 0.103

Gnomad FIN AF: 0.164

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.158

Gnomad OTH AF: 0.181

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

GnomAD4 genome AF: 0.140 AC: 21354 AN: 152206 Hom.: 1696 Cov.: 32 AF XY: 0.140 AC XY: 10441 AN XY: 74420

Gnomad4 AFR AF: 0.0823

Gnomad4 AMR AF: 0.216

Gnomad4 ASJ AF: 0.227

Gnomad4 EAS AF: 0.0605

Gnomad4 SAS AF: 0.103

Gnomad4 FIN AF: 0.164

Gnomad4 NFE AF: 0.158

Gnomad4 OTH AF: 0.187

Alfa AF: 0.167 Hom.: 2245

Bravo AF: 0.140

Asia WGS AF: 0.126 AC: 437 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	2.3
Dann	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12138969; hg19: chr1-207191164;