5-121596154-A-G

Position:

• chr5-121596154-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 0.183 in 151,658 control chromosomes in the GnomAD database, including 3,103 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 0.18 (3103 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.24

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.31 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: 0.183 AC: 27681 AN: 151552 Hom.: 3091 Cov.: 30

Gnomad AFR AF: 0.314

Gnomad AMI AF: 0.144

Gnomad AMR AF: 0.153

Gnomad ASJ AF: 0.0994

Gnomad EAS AF: 0.205

Gnomad SAS AF: 0.110

Gnomad FIN AF: 0.100

Gnomad MID AF: 0.137

Gnomad NFE AF: 0.131

Gnomad OTH AF: 0.180

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

GnomAD4 genome AF: 0.183 AC: 27712 AN: 151658 Hom.: 3103 Cov.: 30 AF XY: 0.181 AC XY: 13419 AN XY: 74124

Gnomad4 AFR AF: 0.315

Gnomad4 AMR AF: 0.152

Gnomad4 ASJ AF: 0.0994

Gnomad4 EAS AF: 0.204

Gnomad4 SAS AF: 0.110

Gnomad4 FIN AF: 0.100

Gnomad4 NFE AF: 0.131

Gnomad4 OTH AF: 0.178

Alfa AF: 0.136 Hom.: 3162

Bravo AF: 0.193

Asia WGS AF: 0.172 AC: 599 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	6.6
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7734808; hg19: chr5-120931849;