rs507369

Variant names:

• chr6-13331828-G-T
• rs507369

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 0.21 in 152,112 control chromosomes in the GnomAD database, including 3,729 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 0.21 (3729 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.518
• Publications: 13 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 = 0.397 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.210 AC: 31931 AN: 151994 Hom.: 3722 Cov.: 32

Gnomad AFR AF: 0.150

Gnomad AMI AF: 0.184

Gnomad AMR AF: 0.285

Gnomad ASJ AF: 0.229

Gnomad EAS AF: 0.125

Gnomad SAS AF: 0.413

Gnomad FIN AF: 0.139

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.233

Gnomad OTH AF: 0.207

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

GnomAD4 genome AF: 0.210 AC: 31960 AN: 152112 Hom.: 3729 Cov.: 32 AF XY: 0.210 AC XY: 15602 AN XY: 74356

African (AFR) AF: 0.150 AC: 6216 AN: 41476

American (AMR) AF: 0.286 AC: 4372 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.229 AC: 795 AN: 3468

East Asian (EAS) AF: 0.126 AC: 651 AN: 5174

South Asian (SAS) AF: 0.412 AC: 1985 AN: 4822

European-Finnish (FIN) AF: 0.139 AC: 1467 AN: 10580

Middle Eastern (MID) AF: 0.207 AC: 61 AN: 294

European-Non Finnish (NFE) AF: 0.233 AC: 15812 AN: 67986

Other (OTH) AF: 0.205 AC: 433 AN: 2114

Alfa AF: 0.205 Hom.: 501

Bravo AF: 0.214

Asia WGS AF: 0.270 AC: 938 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	7.2
DANN	Benign	0.70
PhyloP100		0.52

Splicing

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

Other links and lift over

dbSNP: rs507369; hg19: chr6-13332060;