3-23993497-G-C

Variant names:

• chr3-23993497-G-C
• rs6550826

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;