rs9362636

Variant names:

• chr6-89317078-A-G
• rs9362636

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 0.177 in 152,078 control chromosomes in the GnomAD database, including 4,900 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 0.18 (4900 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.792
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.462 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: 0.176 AC: 26802 AN: 151960 Hom.: 4876 Cov.: 32

Gnomad AFR AF: 0.467

Gnomad AMI AF: 0.0614

Gnomad AMR AF: 0.0863

Gnomad ASJ AF: 0.132

Gnomad EAS AF: 0.118

Gnomad SAS AF: 0.122

Gnomad FIN AF: 0.0391

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.0546

Gnomad OTH AF: 0.154

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

GnomAD4 genome AF: 0.177 AC: 26884 AN: 152078 Hom.: 4900 Cov.: 32 AF XY: 0.173 AC XY: 12882 AN XY: 74360

African (AFR) AF: 0.467 AC: 19346 AN: 41398

American (AMR) AF: 0.0862 AC: 1317 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.132 AC: 459 AN: 3470

East Asian (EAS) AF: 0.118 AC: 610 AN: 5182

South Asian (SAS) AF: 0.122 AC: 587 AN: 4822

European-Finnish (FIN) AF: 0.0391 AC: 415 AN: 10614

Middle Eastern (MID) AF: 0.180 AC: 53 AN: 294

European-Non Finnish (NFE) AF: 0.0546 AC: 3713 AN: 67996

Other (OTH) AF: 0.156 AC: 328 AN: 2108

Alfa AF: 0.0978 Hom.: 5041

Bravo AF: 0.194

Asia WGS AF: 0.141 AC: 493 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.4
DANN	Benign	0.49
PhyloP100		-0.79

Splicing

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

Other links and lift over

dbSNP: rs9362636; hg19: chr6-90026797;