rs764916

chr5-111064493-G-C

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 0.111 in 152,118 control chromosomes in the GnomAD database, including 1,435 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 0.11 (1435 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.168

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.367 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: 0.111 AC: 16814 AN: 152000 Hom.: 1436 Cov.: 33

Gnomad AFR AF: 0.194

Gnomad AMI AF: 0.0515

Gnomad AMR AF: 0.0957

Gnomad ASJ AF: 0.0568

Gnomad EAS AF: 0.382

Gnomad SAS AF: 0.181

Gnomad FIN AF: 0.0653

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0489

Gnomad OTH AF: 0.0896

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

GnomAD4 genome AF: 0.111 AC: 16821 AN: 152118 Hom.: 1435 Cov.: 33 AF XY: 0.115 AC XY: 8525 AN XY: 74376

Gnomad4 AFR AF: 0.194

Gnomad4 AMR AF: 0.0958

Gnomad4 ASJ AF: 0.0568

Gnomad4 EAS AF: 0.381

Gnomad4 SAS AF: 0.182

Gnomad4 FIN AF: 0.0653

Gnomad4 NFE AF: 0.0489

Gnomad4 OTH AF: 0.0882

Alfa AF: 0.0850 Hom.: 119

Bravo AF: 0.116

Asia WGS AF: 0.227 AC: 787 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	3.1
Dann	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs764916; hg19: chr5-110400191;