rs1400142

chr12-73048715-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 0.644 in 151,374 control chromosomes in the GnomAD database, including 31,480 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 0.64 (31480 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.760

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.71 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: 0.644 AC: 97371 AN: 151256 Hom.: 31431 Cov.: 32

Gnomad AFR AF: 0.624

Gnomad AMI AF: 0.682

Gnomad AMR AF: 0.607

Gnomad ASJ AF: 0.586

Gnomad EAS AF: 0.698

Gnomad SAS AF: 0.729

Gnomad FIN AF: 0.652

Gnomad MID AF: 0.694

Gnomad NFE AF: 0.656

Gnomad OTH AF: 0.621

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

GnomAD4 genome AF: 0.644 AC: 97482 AN: 151374 Hom.: 31480 Cov.: 32 AF XY: 0.646 AC XY: 47810 AN XY: 73976

Gnomad4 AFR AF: 0.625

Gnomad4 AMR AF: 0.607

Gnomad4 ASJ AF: 0.586

Gnomad4 EAS AF: 0.697

Gnomad4 SAS AF: 0.730

Gnomad4 FIN AF: 0.652

Gnomad4 NFE AF: 0.656

Gnomad4 OTH AF: 0.622

Alfa AF: 0.653 Hom.: 14951

Bravo AF: 0.630

Asia WGS AF: 0.718 AC: 2495 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	6.0
Dann	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1400142; hg19: chr12-73442495;