rs9327764

Positions:

• chr5-136844388-C-T

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.476

Gnomad4 AMR AF: 0.0855

Gnomad4 ASJ AF: 0.127

Gnomad4 EAS AF: 0.338

Gnomad4 SAS AF: 0.114

Gnomad4 FIN AF: 0.0226

Gnomad4 NFE AF: 0.0235

Gnomad4 OTH AF: 0.143

Alfa AF: 0.0808 Hom.: 412

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9327764; hg19: chr5-136180077;