rs1861478

Variant names:

• chr12-97318901-A-T
• rs1861478

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 0.596 in 151,988 control chromosomes in the GnomAD database, including 27,687 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 0.60 (27687 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.645

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.912 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: 0.597 AC: 90598 AN: 151870 Hom.: 27678 Cov.: 31

Gnomad AFR AF: 0.487

Gnomad AMI AF: 0.564

Gnomad AMR AF: 0.651

Gnomad ASJ AF: 0.659

Gnomad EAS AF: 0.934

Gnomad SAS AF: 0.734

Gnomad FIN AF: 0.673

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.601

Gnomad OTH AF: 0.616

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

GnomAD4 genome AF: 0.596 AC: 90641 AN: 151988 Hom.: 27687 Cov.: 31 AF XY: 0.605 AC XY: 44908 AN XY: 74284

Gnomad4 AFR AF: 0.486

Gnomad4 AMR AF: 0.652

Gnomad4 ASJ AF: 0.659

Gnomad4 EAS AF: 0.934

Gnomad4 SAS AF: 0.735

Gnomad4 FIN AF: 0.673

Gnomad4 NFE AF: 0.601

Gnomad4 OTH AF: 0.615

Alfa AF: 0.589 Hom.: 3314

Bravo AF: 0.590

Asia WGS AF: 0.812 AC: 2825 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.8
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1861478; hg19: chr12-97712679;