chr5-123279830-A-G

Position:

• chr5-123279830-A-G

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 0.0796 in 152,304 control chromosomes in the GnomAD database, including 545 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 0.080 (545 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.694

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.14 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0797 AC: 12123 AN: 152186 Hom.: 544 Cov.: 33

Gnomad AFR AF: 0.0765

Gnomad AMI AF: 0.0559

Gnomad AMR AF: 0.131

Gnomad ASJ AF: 0.0917

Gnomad EAS AF: 0.135

Gnomad SAS AF: 0.149

Gnomad FIN AF: 0.0486

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.0648

Gnomad OTH AF: 0.0968

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

GnomAD4 genome AF: 0.0796 AC: 12129 AN: 152304 Hom.: 545 Cov.: 33 AF XY: 0.0811 AC XY: 6043 AN XY: 74476

Gnomad4 AFR AF: 0.0763

Gnomad4 AMR AF: 0.131

Gnomad4 ASJ AF: 0.0917

Gnomad4 EAS AF: 0.135

Gnomad4 SAS AF: 0.149

Gnomad4 FIN AF: 0.0486

Gnomad4 NFE AF: 0.0648

Gnomad4 OTH AF: 0.101

Alfa AF: 0.0742 Hom.: 143

Bravo AF: 0.0858

Asia WGS AF: 0.171 AC: 593 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.39
DANN	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6881280; hg19: chr5-122615524;