chr3-193708267-T-G

Variant names:

• chr3-193708267-T-G
• rs166812

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 0.487 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.487 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

Gnomad4 AFR AF: 0.557

Gnomad4 AMR AF: 0.376

Gnomad4 ASJ AF: 0.484

Gnomad4 EAS AF: 0.224

Gnomad4 SAS AF: 0.405

Gnomad4 FIN AF: 0.554

Gnomad4 NFE AF: 0.485

Gnomad4 OTH AF: 0.426

Alfa AF: 0.472 Hom.: 17374

Bravo AF: 0.476

Asia WGS AF: 0.332 AC: 1157 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs166812; hg19: chr3-193426056;