rs1400142

Variant names:

• chr12-73048715-C-T
• rs1400142

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;