rs764917

Variant names:

• chr5-111064809-C-A
• rs764917

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 0.604 in 152,020 control chromosomes in the GnomAD database, including 30,202 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 0.60 (30202 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.176

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.869 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: 0.603 AC: 91641 AN: 151902 Hom.: 30150 Cov.: 33

Gnomad AFR AF: 0.876

Gnomad AMI AF: 0.608

Gnomad AMR AF: 0.589

Gnomad ASJ AF: 0.483

Gnomad EAS AF: 0.742

Gnomad SAS AF: 0.571

Gnomad FIN AF: 0.410

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.468

Gnomad OTH AF: 0.593

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

GnomAD4 genome AF: 0.604 AC: 91750 AN: 152020 Hom.: 30202 Cov.: 33 AF XY: 0.602 AC XY: 44687 AN XY: 74286

Gnomad4 AFR AF: 0.876

Gnomad4 AMR AF: 0.588

Gnomad4 ASJ AF: 0.483

Gnomad4 EAS AF: 0.742

Gnomad4 SAS AF: 0.572

Gnomad4 FIN AF: 0.410

Gnomad4 NFE AF: 0.468

Gnomad4 OTH AF: 0.598

Alfa AF: 0.515 Hom.: 4380

Bravo AF: 0.629

Asia WGS AF: 0.681 AC: 2367 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.57
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs764917; hg19: chr5-110400507;