rs1400061

Variant names:

• chr12-73280778-A-C
• rs1400061

Your query was ambiguous. Multiple possible variants found:

• chr12-73280778-A-C
• chr12-73280778-A-G
• chr12-73280778-A-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 0.768 in 151,842 control chromosomes in the GnomAD database, including 45,007 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 0.77 (45007 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.102

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.924 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: 0.768 AC: 116486 AN: 151724 Hom.: 44958 Cov.: 33

Gnomad AFR AF: 0.810

Gnomad AMI AF: 0.738

Gnomad AMR AF: 0.842

Gnomad ASJ AF: 0.670

Gnomad EAS AF: 0.946

Gnomad SAS AF: 0.760

Gnomad FIN AF: 0.715

Gnomad MID AF: 0.804

Gnomad NFE AF: 0.726

Gnomad OTH AF: 0.783

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

GnomAD4 genome AF: 0.768 AC: 116591 AN: 151842 Hom.: 45007 Cov.: 33 AF XY: 0.771 AC XY: 57186 AN XY: 74218

Gnomad4 AFR AF: 0.810

Gnomad4 AMR AF: 0.842

Gnomad4 ASJ AF: 0.670

Gnomad4 EAS AF: 0.946

Gnomad4 SAS AF: 0.760

Gnomad4 FIN AF: 0.715

Gnomad4 NFE AF: 0.726

Gnomad4 OTH AF: 0.785

Alfa AF: 0.734 Hom.: 45322

Bravo AF: 0.781

Asia WGS AF: 0.863 AC: 3000 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.7
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1400061; hg19: chr12-73674558;