3-23993497-G-C

Position:

• chr3-23993497-G-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 0.609 in 151,184 control chromosomes in the GnomAD database, including 28,621 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 0.61 (28621 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01

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 (NFE) allele frequency at 95% confidence interval = 0.684 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: 0.609 AC: 92061 AN: 151068 Hom.: 28599 Cov.: 30

Gnomad AFR AF: 0.482

Gnomad AMI AF: 0.485

Gnomad AMR AF: 0.633

Gnomad ASJ AF: 0.710

Gnomad EAS AF: 0.482

Gnomad SAS AF: 0.607

Gnomad FIN AF: 0.594

Gnomad MID AF: 0.732

Gnomad NFE AF: 0.689

Gnomad OTH AF: 0.628

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

GnomAD4 genome AF: 0.609 AC: 92127 AN: 151184 Hom.: 28621 Cov.: 30 AF XY: 0.606 AC XY: 44765 AN XY: 73830

Gnomad4 AFR AF: 0.483

Gnomad4 AMR AF: 0.633

Gnomad4 ASJ AF: 0.710

Gnomad4 EAS AF: 0.482

Gnomad4 SAS AF: 0.607

Gnomad4 FIN AF: 0.594

Gnomad4 NFE AF: 0.689

Gnomad4 OTH AF: 0.626

Alfa AF: 0.639 Hom.: 3875

Bravo AF: 0.607

Asia WGS AF: 0.548 AC: 1907 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	0.49
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6550826; hg19: chr3-24034988;