chr3-112460632-A-C

Variant names:

• chr3-112460632-A-C
• rs2705511

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;