6-31579203-G-A

Variant names:

• chr6-31579203-G-A
• rs3093671

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 0.0395 in 152,264 control chromosomes in the GnomAD database, including 189 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 0.039 (189 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.570
• Publications: 17 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.155 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: 0.0395 AC: 6003 AN: 152146 Hom.: 190 Cov.: 32

Gnomad AFR AF: 0.0561

Gnomad AMI AF: 0.00877

Gnomad AMR AF: 0.0338

Gnomad ASJ AF: 0.0248

Gnomad EAS AF: 0.0381

Gnomad SAS AF: 0.166

Gnomad FIN AF: 0.0245

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0252

Gnomad OTH AF: 0.0421

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

GnomAD4 genome AF: 0.0395 AC: 6008 AN: 152264 Hom.: 189 Cov.: 32 AF XY: 0.0415 AC XY: 3092 AN XY: 74456

African (AFR) AF: 0.0561 AC: 2329 AN: 41538

American (AMR) AF: 0.0337 AC: 516 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0248 AC: 86 AN: 3472

East Asian (EAS) AF: 0.0380 AC: 197 AN: 5184

South Asian (SAS) AF: 0.165 AC: 795 AN: 4822

European-Finnish (FIN) AF: 0.0245 AC: 260 AN: 10620

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.0252 AC: 1712 AN: 68016

Other (OTH) AF: 0.0436 AC: 92 AN: 2112

Alfa AF: 0.0303 Hom.: 221

Bravo AF: 0.0382

Asia WGS AF: 0.117 AC: 407 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.68
DANN	Benign	0.84
PhyloP100		-0.57

Splicing

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

Other links and lift over

dbSNP: rs3093671; hg19: chr6-31546980;