rs12568930

Positions:

• chr1-22375738-T-C

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 0.207 in 152,204 control chromosomes in the GnomAD database, including 3,767 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 0.21 (3767 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0930

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.49).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.317 is higher than 0.05.

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: 0.207 AC: 31461 AN: 152086 Hom.: 3763 Cov.: 33

Gnomad AFR AF: 0.322

Gnomad AMI AF: 0.153

Gnomad AMR AF: 0.146

Gnomad ASJ AF: 0.184

Gnomad EAS AF: 0.216

Gnomad SAS AF: 0.218

Gnomad FIN AF: 0.0781

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.171

Gnomad OTH AF: 0.196

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

GnomAD4 genome AF: 0.207 AC: 31489 AN: 152204 Hom.: 3767 Cov.: 33 AF XY: 0.200 AC XY: 14892 AN XY: 74430

Gnomad4 AFR AF: 0.322

Gnomad4 AMR AF: 0.146

Gnomad4 ASJ AF: 0.184

Gnomad4 EAS AF: 0.217

Gnomad4 SAS AF: 0.218

Gnomad4 FIN AF: 0.0781

Gnomad4 NFE AF: 0.171

Gnomad4 OTH AF: 0.199

Alfa AF: 0.184 Hom.: 1568

Bravo AF: 0.218

Asia WGS AF: 0.217 AC: 757 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.49
CADD	Benign	16
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12568930; hg19: chr1-22702231;