rs3093668

Variant names:

• chr6-31578718-G-C
• rs3093668

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 0.0358 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
• Publications: 40 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.0322 AC: 1337 AN: 41542

American (AMR) AF: 0.0344 AC: 526 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0473 AC: 164 AN: 3470

East Asian (EAS) AF: 0.0258 AC: 134 AN: 5184

South Asian (SAS) AF: 0.0613 AC: 296 AN: 4826

European-Finnish (FIN) AF: 0.0122 AC: 129 AN: 10598

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.0387 AC: 2634 AN: 68026

Other (OTH) AF: 0.0407 AC: 86 AN: 2114

Alfa AF: 0.0366 Hom.: 11

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
PhyloP100		1.8

Splicing

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

Other links and lift over

dbSNP: rs3093668; hg19: chr6-31546495;