rs12076751

chr1-43327136-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 0.326 in 151,934 control chromosomes in the GnomAD database, including 8,433 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 0.33 (8433 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.53

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.37 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: 0.326 AC: 49457 AN: 151816 Hom.: 8427 Cov.: 31

Gnomad AFR AF: 0.265

Gnomad AMI AF: 0.387

Gnomad AMR AF: 0.375

Gnomad ASJ AF: 0.413

Gnomad EAS AF: 0.0984

Gnomad SAS AF: 0.148

Gnomad FIN AF: 0.331

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.374

Gnomad OTH AF: 0.376

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

GnomAD4 genome AF: 0.326 AC: 49496 AN: 151934 Hom.: 8433 Cov.: 31 AF XY: 0.321 AC XY: 23855 AN XY: 74278

Gnomad4 AFR AF: 0.265

Gnomad4 AMR AF: 0.375

Gnomad4 ASJ AF: 0.413

Gnomad4 EAS AF: 0.0983

Gnomad4 SAS AF: 0.149

Gnomad4 FIN AF: 0.331

Gnomad4 NFE AF: 0.374

Gnomad4 OTH AF: 0.374

Alfa AF: 0.350 Hom.: 1983

Bravo AF: 0.328

Asia WGS AF: 0.148 AC: 515 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	0.36
Dann	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12076751; hg19: chr1-43792807;