chr3-112460632-A-C

Position:

• chr3-112460632-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 0.315 in 152,036 control chromosomes in the GnomAD database, including 8,443 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 0.32 (8443 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0700

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.71 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.315 AC: 47864 AN: 151918 Hom.: 8411 Cov.: 32

Gnomad AFR AF: 0.352

Gnomad AMI AF: 0.318

Gnomad AMR AF: 0.378

Gnomad ASJ AF: 0.233

Gnomad EAS AF: 0.729

Gnomad SAS AF: 0.517

Gnomad FIN AF: 0.314

Gnomad MID AF: 0.376

Gnomad NFE AF: 0.237

Gnomad OTH AF: 0.288

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

GnomAD4 genome AF: 0.315 AC: 47946 AN: 152036 Hom.: 8443 Cov.: 32 AF XY: 0.325 AC XY: 24128 AN XY: 74312

Gnomad4 AFR AF: 0.352

Gnomad4 AMR AF: 0.380

Gnomad4 ASJ AF: 0.233

Gnomad4 EAS AF: 0.729

Gnomad4 SAS AF: 0.517

Gnomad4 FIN AF: 0.314

Gnomad4 NFE AF: 0.237

Gnomad4 OTH AF: 0.294

Alfa AF: 0.146 Hom.: 268

Bravo AF: 0.322

Asia WGS AF: 0.595 AC: 2064 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.8
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2705511; hg19: chr3-112179479;