3-23702595-A-G

Position:

• chr3-23702595-A-G

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 0.564 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.564 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

Gnomad4 AFR AF: 0.785

Gnomad4 AMR AF: 0.505

Gnomad4 ASJ AF: 0.556

Gnomad4 EAS AF: 0.311

Gnomad4 SAS AF: 0.484

Gnomad4 FIN AF: 0.441

Gnomad4 NFE AF: 0.487

Gnomad4 OTH AF: 0.572

Alfa AF: 0.509 Hom.: 27882

Bravo AF: 0.577

Asia WGS AF: 0.432 AC: 1503 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6550783; hg19: chr3-23744086;