rs3093993

Variant names:

• chr6-31522948-C-A
• rs3093993

Your query was ambiguous. Multiple possible variants found:

• chr6-31522948-C-A
• chr6-31522948-C-G
• chr6-31522948-C-T

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 0.791 in 152,214 control chromosomes in the GnomAD database, including 47,795 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 0.79 (47795 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0180
• Publications: 36 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.6).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.878 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: 0.791 AC: 120380 AN: 152096 Hom.: 47754 Cov.: 32

Gnomad AFR AF: 0.822

Gnomad AMI AF: 0.669

Gnomad AMR AF: 0.812

Gnomad ASJ AF: 0.859

Gnomad EAS AF: 0.899

Gnomad SAS AF: 0.860

Gnomad FIN AF: 0.807

Gnomad MID AF: 0.864

Gnomad NFE AF: 0.751

Gnomad OTH AF: 0.787

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

GnomAD4 genome AF: 0.791 AC: 120474 AN: 152214 Hom.: 47795 Cov.: 32 AF XY: 0.797 AC XY: 59322 AN XY: 74420

African (AFR) AF: 0.822 AC: 34128 AN: 41528

American (AMR) AF: 0.812 AC: 12423 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.859 AC: 2983 AN: 3472

East Asian (EAS) AF: 0.900 AC: 4664 AN: 5184

South Asian (SAS) AF: 0.861 AC: 4156 AN: 4826

European-Finnish (FIN) AF: 0.807 AC: 8547 AN: 10588

Middle Eastern (MID) AF: 0.857 AC: 252 AN: 294

European-Non Finnish (NFE) AF: 0.751 AC: 51046 AN: 68002

Other (OTH) AF: 0.789 AC: 1668 AN: 2114

Alfa AF: 0.772 Hom.: 131731

Bravo AF: 0.792

Asia WGS AF: 0.823 AC: 2865 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.60
CADD	Benign	14
DANN	Benign	0.89
PhyloP100		0.018

Splicing

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

Other links and lift over

dbSNP: rs3093993; hg19: chr6-31490725;