chr3-112500489-C-T

Position:

• chr3-112500489-C-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 0.158 in 151,974 control chromosomes in the GnomAD database, including 3,973 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 0.16 (3973 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0840

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 (AFR) allele frequency at 95% confidence interval = 0.41 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: 0.158 AC: 23934 AN: 151856 Hom.: 3968 Cov.: 32

Gnomad AFR AF: 0.415

Gnomad AMI AF: 0.0154

Gnomad AMR AF: 0.146

Gnomad ASJ AF: 0.0493

Gnomad EAS AF: 0.186

Gnomad SAS AF: 0.126

Gnomad FIN AF: 0.0255

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.0333

Gnomad OTH AF: 0.132

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

GnomAD4 genome AF: 0.158 AC: 23970 AN: 151974 Hom.: 3973 Cov.: 32 AF XY: 0.157 AC XY: 11668 AN XY: 74324

Gnomad4 AFR AF: 0.415

Gnomad4 AMR AF: 0.145

Gnomad4 ASJ AF: 0.0493

Gnomad4 EAS AF: 0.186

Gnomad4 SAS AF: 0.125

Gnomad4 FIN AF: 0.0255

Gnomad4 NFE AF: 0.0333

Gnomad4 OTH AF: 0.130

Alfa AF: 0.110 Hom.: 375

Bravo AF: 0.181

Asia WGS AF: 0.139 AC: 483 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.7
DANN	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2705565; hg19: chr3-112219336;