3-193708267-T-G

Variant names:

• chr3-193708267-T-G
• rs166812

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 0.487 in 151,980 control chromosomes in the GnomAD database, including 18,549 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 0.49 (18549 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.651
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.551 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.487 AC: 73931 AN: 151862 Hom.: 18541 Cov.: 32

Gnomad AFR AF: 0.557

Gnomad AMI AF: 0.574

Gnomad AMR AF: 0.377

Gnomad ASJ AF: 0.484

Gnomad EAS AF: 0.224

Gnomad SAS AF: 0.406

Gnomad FIN AF: 0.554

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.485

Gnomad OTH AF: 0.429

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

GnomAD4 genome AF: 0.487 AC: 73970 AN: 151980 Hom.: 18549 Cov.: 32 AF XY: 0.484 AC XY: 35971 AN XY: 74298

African (AFR) AF: 0.557 AC: 23101 AN: 41446

American (AMR) AF: 0.376 AC: 5746 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.484 AC: 1676 AN: 3464

East Asian (EAS) AF: 0.224 AC: 1161 AN: 5182

South Asian (SAS) AF: 0.405 AC: 1948 AN: 4810

European-Finnish (FIN) AF: 0.554 AC: 5850 AN: 10564

Middle Eastern (MID) AF: 0.466 AC: 136 AN: 292

European-Non Finnish (NFE) AF: 0.485 AC: 32935 AN: 67944

Other (OTH) AF: 0.426 AC: 897 AN: 2108

Alfa AF: 0.473 Hom.: 22670

Bravo AF: 0.476

Asia WGS AF: 0.332 AC: 1157 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.82
DANN	Benign	0.57
PhyloP100		-0.65

Splicing

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

Other links and lift over

dbSNP: rs166812; hg19: chr3-193426056;