3-55356858-G-T

Position:

• chr3-55356858-G-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 0.0971 in 152,226 control chromosomes in the GnomAD database, including 856 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 0.097 (856 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0230

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.13 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: 0.0971 AC: 14777 AN: 152108 Hom.: 857 Cov.: 32

Gnomad AFR AF: 0.0488

Gnomad AMI AF: 0.211

Gnomad AMR AF: 0.0919

Gnomad ASJ AF: 0.167

Gnomad EAS AF: 0.00386

Gnomad SAS AF: 0.0584

Gnomad FIN AF: 0.0948

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.132

Gnomad OTH AF: 0.112

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

GnomAD4 genome AF: 0.0971 AC: 14774 AN: 152226 Hom.: 856 Cov.: 32 AF XY: 0.0932 AC XY: 6935 AN XY: 74424

Gnomad4 AFR AF: 0.0488

Gnomad4 AMR AF: 0.0917

Gnomad4 ASJ AF: 0.167

Gnomad4 EAS AF: 0.00386

Gnomad4 SAS AF: 0.0578

Gnomad4 FIN AF: 0.0948

Gnomad4 NFE AF: 0.132

Gnomad4 OTH AF: 0.111

Alfa AF: 0.128 Hom.: 1260

Bravo AF: 0.0960

Asia WGS AF: 0.0280 AC: 99 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.44
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11925054; hg19: chr3-55390886;