chr5-9928750-A-C

Position:

• chr5-9928750-A-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 0.0677 in 152,102 control chromosomes in the GnomAD database, including 519 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 0.068 (519 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.711

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.214 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: 0.0678 AC: 10300 AN: 151984 Hom.: 520 Cov.: 32

Gnomad AFR AF: 0.0324

Gnomad AMI AF: 0.121

Gnomad AMR AF: 0.103

Gnomad ASJ AF: 0.105

Gnomad EAS AF: 0.191

Gnomad SAS AF: 0.224

Gnomad FIN AF: 0.0378

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0629

Gnomad OTH AF: 0.0652

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

GnomAD4 genome AF: 0.0677 AC: 10303 AN: 152102 Hom.: 519 Cov.: 32 AF XY: 0.0704 AC XY: 5235 AN XY: 74330

Gnomad4 AFR AF: 0.0324

Gnomad4 AMR AF: 0.103

Gnomad4 ASJ AF: 0.105

Gnomad4 EAS AF: 0.190

Gnomad4 SAS AF: 0.225

Gnomad4 FIN AF: 0.0378

Gnomad4 NFE AF: 0.0629

Gnomad4 OTH AF: 0.0674

Alfa AF: 0.0682 Hom.: 600

Bravo AF: 0.0694

Asia WGS AF: 0.196 AC: 680 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	3.1
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1035961; hg19: chr5-9928862;