rs13068101

Variant names:

• chr3-193054506-G-A
• rs13068101

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 0.193 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.193 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

Gnomad4 AFR AF: 0.0474

Gnomad4 AMR AF: 0.254

Gnomad4 ASJ AF: 0.276

Gnomad4 EAS AF: 0.174

Gnomad4 SAS AF: 0.123

Gnomad4 FIN AF: 0.251

Gnomad4 NFE AF: 0.260

Gnomad4 OTH AF: 0.204

Alfa AF: 0.253 Hom.: 10274

Bravo AF: 0.193

Asia WGS AF: 0.145 AC: 504 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13068101; hg19: chr3-192772295;