rs9359765

Variant names:

• chr6-88116718-C-T
• rs9359765

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 0.392 in 152,116 control chromosomes in the GnomAD database, including 14,645 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 0.39 (14645 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0990
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.692 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: 0.392 AC: 59522 AN: 151996 Hom.: 14631 Cov.: 32

Gnomad AFR AF: 0.699

Gnomad AMI AF: 0.275

Gnomad AMR AF: 0.278

Gnomad ASJ AF: 0.212

Gnomad EAS AF: 0.112

Gnomad SAS AF: 0.182

Gnomad FIN AF: 0.314

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.291

Gnomad OTH AF: 0.340

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

GnomAD4 genome AF: 0.392 AC: 59582 AN: 152116 Hom.: 14645 Cov.: 32 AF XY: 0.384 AC XY: 28588 AN XY: 74356

African (AFR) AF: 0.698 AC: 28970 AN: 41476

American (AMR) AF: 0.278 AC: 4255 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.212 AC: 737 AN: 3470

East Asian (EAS) AF: 0.112 AC: 582 AN: 5190

South Asian (SAS) AF: 0.181 AC: 875 AN: 4824

European-Finnish (FIN) AF: 0.314 AC: 3316 AN: 10558

Middle Eastern (MID) AF: 0.259 AC: 76 AN: 294

European-Non Finnish (NFE) AF: 0.291 AC: 19813 AN: 67990

Other (OTH) AF: 0.335 AC: 708 AN: 2114

Alfa AF: 0.316 Hom.: 26612

Bravo AF: 0.400

Asia WGS AF: 0.169 AC: 590 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.5
DANN	Benign	0.43
PhyloP100		0.099

Splicing

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

Other links and lift over

dbSNP: rs9359765; hg19: chr6-88826436;