rs12751302

chr1-191577444-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 0.29 in 151,774 control chromosomes in the GnomAD database, including 7,175 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 0.29 (7175 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.337

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.373 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: 0.291 AC: 44058 AN: 151658 Hom.: 7174 Cov.: 30

Gnomad AFR AF: 0.139

Gnomad AMI AF: 0.218

Gnomad AMR AF: 0.297

Gnomad ASJ AF: 0.441

Gnomad EAS AF: 0.236

Gnomad SAS AF: 0.387

Gnomad FIN AF: 0.390

Gnomad MID AF: 0.395

Gnomad NFE AF: 0.355

Gnomad OTH AF: 0.328

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

GnomAD4 genome AF: 0.290 AC: 44070 AN: 151774 Hom.: 7175 Cov.: 30 AF XY: 0.293 AC XY: 21730 AN XY: 74154

Gnomad4 AFR AF: 0.139

Gnomad4 AMR AF: 0.296

Gnomad4 ASJ AF: 0.441

Gnomad4 EAS AF: 0.236

Gnomad4 SAS AF: 0.387

Gnomad4 FIN AF: 0.390

Gnomad4 NFE AF: 0.355

Gnomad4 OTH AF: 0.330

Alfa AF: 0.342 Hom.: 4196

Bravo AF: 0.275

Asia WGS AF: 0.312 AC: 1082 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	3.1
Dann	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12751302; hg19: chr1-191546574;