rs1526805

Positions:

• chr12-74990857-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 0.0933 in 151,482 control chromosomes in the GnomAD database, including 864 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 0.093 (864 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.66

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.205 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: 0.0934 AC: 14133 AN: 151374 Hom.: 863 Cov.: 31

Gnomad AFR AF: 0.123

Gnomad AMI AF: 0.0241

Gnomad AMR AF: 0.138

Gnomad ASJ AF: 0.151

Gnomad EAS AF: 0.215

Gnomad SAS AF: 0.214

Gnomad FIN AF: 0.0355

Gnomad MID AF: 0.182

Gnomad NFE AF: 0.0539

Gnomad OTH AF: 0.0986

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

GnomAD4 genome AF: 0.0933 AC: 14135 AN: 151482 Hom.: 864 Cov.: 31 AF XY: 0.0966 AC XY: 7147 AN XY: 74010

Gnomad4 AFR AF: 0.123

Gnomad4 AMR AF: 0.138

Gnomad4 ASJ AF: 0.151

Gnomad4 EAS AF: 0.215

Gnomad4 SAS AF: 0.213

Gnomad4 FIN AF: 0.0355

Gnomad4 NFE AF: 0.0539

Gnomad4 OTH AF: 0.0971

Alfa AF: 0.0729 Hom.: 106

Bravo AF: 0.104

Asia WGS AF: 0.172 AC: 598 AN: 3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.055
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1526805; hg19: chr12-75384637;