rs12751302

Variant names:

• chr1-191577444-C-T
• rs12751302

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.139 AC: 5772 AN: 41448

American (AMR) AF: 0.296 AC: 4492 AN: 15172

Ashkenazi Jewish (ASJ) AF: 0.441 AC: 1528 AN: 3468

East Asian (EAS) AF: 0.236 AC: 1216 AN: 5146

South Asian (SAS) AF: 0.387 AC: 1868 AN: 4824

European-Finnish (FIN) AF: 0.390 AC: 4108 AN: 10538

Middle Eastern (MID) AF: 0.390 AC: 114 AN: 292

European-Non Finnish (NFE) AF: 0.355 AC: 24080 AN: 67874

Other (OTH) AF: 0.330 AC: 694 AN: 2102

Alfa AF: 0.343 Hom.: 4662

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
PhyloP100		-0.34

Splicing

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

Other links and lift over

dbSNP: rs12751302; hg19: chr1-191546574;