3-23702595-A-G

Variant names:

• chr3-23702595-A-G
• rs6550783

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.564 in 152,190 control chromosomes in the GnomAD database, including 25,678 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 0.56 (25678 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00500
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.778 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.564 AC: 85706 AN: 152070 Hom.: 25633 Cov.: 32

Gnomad AFR AF: 0.784

Gnomad AMI AF: 0.443

Gnomad AMR AF: 0.505

Gnomad ASJ AF: 0.556

Gnomad EAS AF: 0.311

Gnomad SAS AF: 0.486

Gnomad FIN AF: 0.441

Gnomad MID AF: 0.642

Gnomad NFE AF: 0.487

Gnomad OTH AF: 0.574

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

GnomAD4 genome AF: 0.564 AC: 85807 AN: 152190 Hom.: 25678 Cov.: 32 AF XY: 0.559 AC XY: 41558 AN XY: 74406

African (AFR) AF: 0.785 AC: 32605 AN: 41552

American (AMR) AF: 0.505 AC: 7724 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.556 AC: 1928 AN: 3466

East Asian (EAS) AF: 0.311 AC: 1608 AN: 5170

South Asian (SAS) AF: 0.484 AC: 2338 AN: 4828

European-Finnish (FIN) AF: 0.441 AC: 4667 AN: 10584

Middle Eastern (MID) AF: 0.650 AC: 191 AN: 294

European-Non Finnish (NFE) AF: 0.487 AC: 33132 AN: 67978

Other (OTH) AF: 0.572 AC: 1210 AN: 2116

Alfa AF: 0.511 Hom.: 33557

Bravo AF: 0.577

Asia WGS AF: 0.432 AC: 1503 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	5.1
DANN	Benign	0.76
PhyloP100		-0.0050

Splicing

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

Other links and lift over

dbSNP: rs6550783; hg19: chr3-23744086;