chr5-117312029-A-G

Position:

• chr5-117312029-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 0.127 in 151,932 control chromosomes in the GnomAD database, including 1,538 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 0.13 (1538 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.640

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.21 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: 0.127 AC: 19271 AN: 151814 Hom.: 1530 Cov.: 32

Gnomad AFR AF: 0.214

Gnomad AMI AF: 0.0396

Gnomad AMR AF: 0.131

Gnomad ASJ AF: 0.149

Gnomad EAS AF: 0.0892

Gnomad SAS AF: 0.0777

Gnomad FIN AF: 0.0940

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.0848

Gnomad OTH AF: 0.128

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

GnomAD4 genome AF: 0.127 AC: 19322 AN: 151932 Hom.: 1538 Cov.: 32 AF XY: 0.126 AC XY: 9387 AN XY: 74280

Gnomad4 AFR AF: 0.214

Gnomad4 AMR AF: 0.131

Gnomad4 ASJ AF: 0.149

Gnomad4 EAS AF: 0.0894

Gnomad4 SAS AF: 0.0780

Gnomad4 FIN AF: 0.0940

Gnomad4 NFE AF: 0.0848

Gnomad4 OTH AF: 0.132

Alfa AF: 0.0974 Hom.: 1178

Bravo AF: 0.134

Asia WGS AF: 0.109 AC: 376 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	8.2
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7735145; hg19: chr5-116647725;