3-1555373-T-C

Variant names:

• chr3-1555373-T-C
• rs11712183

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 0.35 in 152,036 control chromosomes in the GnomAD database, including 10,945 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 0.35 (10945 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0160
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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 = 0.566 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.349 AC: 53072 AN: 151918 Hom.: 10900 Cov.: 32

Gnomad AFR AF: 0.571

Gnomad AMI AF: 0.414

Gnomad AMR AF: 0.295

Gnomad ASJ AF: 0.323

Gnomad EAS AF: 0.390

Gnomad SAS AF: 0.281

Gnomad FIN AF: 0.206

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.252

Gnomad OTH AF: 0.331

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

GnomAD4 genome AF: 0.350 AC: 53158 AN: 152036 Hom.: 10945 Cov.: 32 AF XY: 0.345 AC XY: 25633 AN XY: 74310

African (AFR) AF: 0.572 AC: 23696 AN: 41456

American (AMR) AF: 0.294 AC: 4481 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.323 AC: 1120 AN: 3472

East Asian (EAS) AF: 0.389 AC: 2008 AN: 5156

South Asian (SAS) AF: 0.280 AC: 1350 AN: 4826

European-Finnish (FIN) AF: 0.206 AC: 2176 AN: 10582

Middle Eastern (MID) AF: 0.357 AC: 105 AN: 294

European-Non Finnish (NFE) AF: 0.252 AC: 17145 AN: 67968

Other (OTH) AF: 0.332 AC: 702 AN: 2114

Alfa AF: 0.281 Hom.: 11667

Bravo AF: 0.368

Asia WGS AF: 0.381 AC: 1326 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.4
DANN	Benign	0.67
PhyloP100		-0.016

Splicing

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

Other links and lift over

dbSNP: rs11712183; hg19: chr3-1597057;