3-55462232-C-T

Variant names:

• chr3-55462232-C-T
• rs11706227

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 8 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.0249 AC: 1032 AN: 41524

American (AMR) AF: 0.0755 AC: 1155 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.106 AC: 369 AN: 3472

East Asian (EAS) AF: 0.000967 AC: 5 AN: 5172

South Asian (SAS) AF: 0.101 AC: 487 AN: 4824

European-Finnish (FIN) AF: 0.232 AC: 2453 AN: 10584

Middle Eastern (MID) AF: 0.110 AC: 32 AN: 292

European-Non Finnish (NFE) AF: 0.148 AC: 10027 AN: 67976

Other (OTH) AF: 0.0838 AC: 177 AN: 2112

Alfa AF: 0.123 Hom.: 4207

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
PhyloP100		-3.1

Splicing

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

Other links and lift over

dbSNP: rs11706227; hg19: chr3-55496260;