rs9395769

Variant names:

• chr6-52191687-G-A
• rs9395769

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 0.12 in 152,042 control chromosomes in the GnomAD database, including 1,180 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 0.12 (1180 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.530
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.153 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: 0.120 AC: 18271 AN: 151924 Hom.: 1180 Cov.: 31

Gnomad AFR AF: 0.0855

Gnomad AMI AF: 0.171

Gnomad AMR AF: 0.0914

Gnomad ASJ AF: 0.221

Gnomad EAS AF: 0.0451

Gnomad SAS AF: 0.163

Gnomad FIN AF: 0.150

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.140

Gnomad OTH AF: 0.131

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

GnomAD4 genome AF: 0.120 AC: 18281 AN: 152042 Hom.: 1180 Cov.: 31 AF XY: 0.121 AC XY: 9024 AN XY: 74294

African (AFR) AF: 0.0855 AC: 3548 AN: 41486

American (AMR) AF: 0.0913 AC: 1396 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.221 AC: 766 AN: 3470

East Asian (EAS) AF: 0.0450 AC: 232 AN: 5160

South Asian (SAS) AF: 0.163 AC: 781 AN: 4802

European-Finnish (FIN) AF: 0.150 AC: 1583 AN: 10560

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.140 AC: 9504 AN: 67958

Other (OTH) AF: 0.130 AC: 276 AN: 2116

Alfa AF: 0.130 Hom.: 331

Bravo AF: 0.113

Asia WGS AF: 0.0890 AC: 307 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.1
DANN	Benign	0.64
PhyloP100		-0.53

Splicing

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

Other links and lift over

dbSNP: rs9395769; hg19: chr6-52056485;