rs1179246

chr12-68246803-A-C

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 0.488 in 152,086 control chromosomes in the GnomAD database, including 18,574 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 0.49 (18574 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.639

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.586 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: 0.487 AC: 74080 AN: 151968 Hom.: 18539 Cov.: 32

Gnomad AFR AF: 0.580

Gnomad AMI AF: 0.454

Gnomad AMR AF: 0.485

Gnomad ASJ AF: 0.572

Gnomad EAS AF: 0.516

Gnomad SAS AF: 0.605

Gnomad FIN AF: 0.463

Gnomad MID AF: 0.614

Gnomad NFE AF: 0.419

Gnomad OTH AF: 0.521

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

GnomAD4 genome AF: 0.488 AC: 74172 AN: 152086 Hom.: 18574 Cov.: 32 AF XY: 0.491 AC XY: 36473 AN XY: 74336

Gnomad4 AFR AF: 0.580

Gnomad4 AMR AF: 0.485

Gnomad4 ASJ AF: 0.572

Gnomad4 EAS AF: 0.516

Gnomad4 SAS AF: 0.604

Gnomad4 FIN AF: 0.463

Gnomad4 NFE AF: 0.420

Gnomad4 OTH AF: 0.527

Alfa AF: 0.454 Hom.: 16597

Bravo AF: 0.496

Asia WGS AF: 0.595 AC: 2066 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.4
Dann	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1179246; hg19: chr12-68640583;