rs9395769

Variant names:

• chr6-52191687-G-A
• rs9395769

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.120 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

Gnomad4 AFR AF: 0.0855

Gnomad4 AMR AF: 0.0913

Gnomad4 ASJ AF: 0.221

Gnomad4 EAS AF: 0.0450

Gnomad4 SAS AF: 0.163

Gnomad4 FIN AF: 0.150

Gnomad4 NFE AF: 0.140

Gnomad4 OTH AF: 0.130

Alfa AF: 0.130 Hom.: 326

Bravo AF: 0.113

Asia WGS AF: 0.0890 AC: 307 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9395769; hg19: chr6-52056485;