chr3-55462232-C-T

Position:

• chr3-55462232-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 0.104 in 152,174 control chromosomes in the GnomAD database, including 1,141 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 0.10 (1141 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.15

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.145 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: 0.104 AC: 15833 AN: 152054 Hom.: 1141 Cov.: 32

Gnomad AFR AF: 0.0249

Gnomad AMI AF: 0.103

Gnomad AMR AF: 0.0756

Gnomad ASJ AF: 0.106

Gnomad EAS AF: 0.000965

Gnomad SAS AF: 0.100

Gnomad FIN AF: 0.232

Gnomad MID AF: 0.109

Gnomad NFE AF: 0.148

Gnomad OTH AF: 0.0856

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

GnomAD4 genome AF: 0.104 AC: 15831 AN: 152174 Hom.: 1141 Cov.: 32 AF XY: 0.107 AC XY: 7980 AN XY: 74402

Gnomad4 AFR AF: 0.0249

Gnomad4 AMR AF: 0.0755

Gnomad4 ASJ AF: 0.106

Gnomad4 EAS AF: 0.000967

Gnomad4 SAS AF: 0.101

Gnomad4 FIN AF: 0.232

Gnomad4 NFE AF: 0.148

Gnomad4 OTH AF: 0.0838

Alfa AF: 0.129 Hom.: 2918

Bravo AF: 0.0860

Asia WGS AF: 0.0510 AC: 175 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.050
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11706227; hg19: chr3-55496260;