chr3-23152437-G-A

Position:

• chr3-23152437-G-A

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 0.766 in 152,018 control chromosomes in the GnomAD database, including 45,588 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 0.77 (45588 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0180

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.926 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: 0.766 AC: 116385 AN: 151900 Hom.: 45513 Cov.: 31

Gnomad AFR AF: 0.934

Gnomad AMI AF: 0.876

Gnomad AMR AF: 0.766

Gnomad ASJ AF: 0.558

Gnomad EAS AF: 0.821

Gnomad SAS AF: 0.738

Gnomad FIN AF: 0.733

Gnomad MID AF: 0.640

Gnomad NFE AF: 0.678

Gnomad OTH AF: 0.726

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

GnomAD4 genome AF: 0.766 AC: 116518 AN: 152018 Hom.: 45588 Cov.: 31 AF XY: 0.770 AC XY: 57190 AN XY: 74288

Gnomad4 AFR AF: 0.934

Gnomad4 AMR AF: 0.766

Gnomad4 ASJ AF: 0.558

Gnomad4 EAS AF: 0.821

Gnomad4 SAS AF: 0.738

Gnomad4 FIN AF: 0.733

Gnomad4 NFE AF: 0.678

Gnomad4 OTH AF: 0.731

Alfa AF: 0.691 Hom.: 49226

Bravo AF: 0.778

Asia WGS AF: 0.818 AC: 2845 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.60
DANN	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4619807; hg19: chr3-23193928;