chr3-89525702-C-T

Position:

• chr3-89525702-C-T

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 0.205 in 151,950 control chromosomes in the GnomAD database, including 3,906 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 0.20 (3906 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.528

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.52).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.263 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: 0.205 AC: 31082 AN: 151830 Hom.: 3907 Cov.: 32

Gnomad AFR AF: 0.0943

Gnomad AMI AF: 0.0735

Gnomad AMR AF: 0.195

Gnomad ASJ AF: 0.148

Gnomad EAS AF: 0.0875

Gnomad SAS AF: 0.0921

Gnomad FIN AF: 0.404

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.266

Gnomad OTH AF: 0.179

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

GnomAD4 genome AF: 0.205 AC: 31091 AN: 151950 Hom.: 3906 Cov.: 32 AF XY: 0.206 AC XY: 15315 AN XY: 74256

Gnomad4 AFR AF: 0.0944

Gnomad4 AMR AF: 0.195

Gnomad4 ASJ AF: 0.148

Gnomad4 EAS AF: 0.0878

Gnomad4 SAS AF: 0.0916

Gnomad4 FIN AF: 0.404

Gnomad4 NFE AF: 0.266

Gnomad4 OTH AF: 0.176

Alfa AF: 0.240 Hom.: 2228

Bravo AF: 0.185

Asia WGS AF: 0.0900 AC: 312 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.52
CADD	Benign	9.7
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs907548; hg19: chr3-89574852;