rs3093668

chr6-31578718-G-C

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 0.0358 in 152,258 control chromosomes in the GnomAD database, including 105 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 0.036 (105 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.78

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.64).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0556 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0357 AC: 5436 AN: 152140 Hom.: 102 Cov.: 32

Gnomad AFR AF: 0.0317

Gnomad AMI AF: 0.153

Gnomad AMR AF: 0.0343

Gnomad ASJ AF: 0.0473

Gnomad EAS AF: 0.0258

Gnomad SAS AF: 0.0621

Gnomad FIN AF: 0.0122

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0387

Gnomad OTH AF: 0.0411

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

GnomAD4 genome AF: 0.0358 AC: 5455 AN: 152258 Hom.: 105 Cov.: 32 AF XY: 0.0357 AC XY: 2661 AN XY: 74446

Gnomad4 AFR AF: 0.0322

Gnomad4 AMR AF: 0.0344

Gnomad4 ASJ AF: 0.0473

Gnomad4 EAS AF: 0.0258

Gnomad4 SAS AF: 0.0613

Gnomad4 FIN AF: 0.0122

Gnomad4 NFE AF: 0.0387

Gnomad4 OTH AF: 0.0407

Alfa AF: 0.0386 Hom.: 10

Bravo AF: 0.0364

Asia WGS AF: 0.0410 AC: 143 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
Cadd	Benign	8.2
Dann	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3093668; hg19: chr6-31546495;