rs9327764

Variant names:

• chr5-136844388-C-T
• rs9327764

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.171 in 152,080 control chromosomes in the GnomAD database, including 5,223 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 0.17 (5223 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.19
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.44).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.471 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: 0.171 AC: 25958 AN: 151962 Hom.: 5213 Cov.: 32

Gnomad AFR AF: 0.477

Gnomad AMI AF: 0.0275

Gnomad AMR AF: 0.0857

Gnomad ASJ AF: 0.127

Gnomad EAS AF: 0.337

Gnomad SAS AF: 0.113

Gnomad FIN AF: 0.0226

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.0235

Gnomad OTH AF: 0.140

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

GnomAD4 genome AF: 0.171 AC: 26003 AN: 152080 Hom.: 5223 Cov.: 32 AF XY: 0.168 AC XY: 12503 AN XY: 74354

African (AFR) AF: 0.476 AC: 19743 AN: 41452

American (AMR) AF: 0.0855 AC: 1305 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.127 AC: 440 AN: 3472

East Asian (EAS) AF: 0.338 AC: 1744 AN: 5156

South Asian (SAS) AF: 0.114 AC: 551 AN: 4824

European-Finnish (FIN) AF: 0.0226 AC: 239 AN: 10598

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

European-Non Finnish (NFE) AF: 0.0235 AC: 1601 AN: 67992

Other (OTH) AF: 0.143 AC: 302 AN: 2110

Alfa AF: 0.0898 Hom.: 495

Bravo AF: 0.190

Asia WGS AF: 0.238 AC: 825 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.44
CADD	Benign	19
DANN	Benign	0.53
PhyloP100		3.2

Splicing

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

Other links and lift over

dbSNP: rs9327764; hg19: chr5-136180077;