chr5-121596154-A-G

Variant names:

• chr5-121596154-A-G
• rs7734808

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;