3-193054506-G-A

Variant names:

• chr3-193054506-G-A
• rs13068101

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 0.193 in 152,056 control chromosomes in the GnomAD database, including 3,537 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 0.19 (3537 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.40
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.257 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: 0.193 AC: 29387 AN: 151938 Hom.: 3537 Cov.: 32

Gnomad AFR AF: 0.0475

Gnomad AMI AF: 0.265

Gnomad AMR AF: 0.254

Gnomad ASJ AF: 0.276

Gnomad EAS AF: 0.174

Gnomad SAS AF: 0.123

Gnomad FIN AF: 0.251

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.260

Gnomad OTH AF: 0.205

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

GnomAD4 genome AF: 0.193 AC: 29387 AN: 152056 Hom.: 3537 Cov.: 32 AF XY: 0.193 AC XY: 14319 AN XY: 74328

African (AFR) AF: 0.0474 AC: 1967 AN: 41488

American (AMR) AF: 0.254 AC: 3888 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.276 AC: 956 AN: 3464

East Asian (EAS) AF: 0.174 AC: 900 AN: 5176

South Asian (SAS) AF: 0.123 AC: 593 AN: 4822

European-Finnish (FIN) AF: 0.251 AC: 2653 AN: 10552

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.260 AC: 17694 AN: 67948

Other (OTH) AF: 0.204 AC: 431 AN: 2110

Alfa AF: 0.242 Hom.: 15264

Bravo AF: 0.193

Asia WGS AF: 0.145 AC: 504 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	8.1
DANN	Benign	0.93
PhyloP100		1.4

Splicing

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

Other links and lift over

dbSNP: rs13068101; hg19: chr3-192772295;