chr5-162404815-G-A

Position:

• chr5-162404815-G-A

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 0.167 in 151,940 control chromosomes in the GnomAD database, including 2,235 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 0.17 (2235 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.197

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 (AMR) allele frequency at 95% confidence interval = 0.218 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: 0.167 AC: 25320 AN: 151822 Hom.: 2230 Cov.: 32

Gnomad AFR AF: 0.174

Gnomad AMI AF: 0.246

Gnomad AMR AF: 0.224

Gnomad ASJ AF: 0.140

Gnomad EAS AF: 0.0804

Gnomad SAS AF: 0.115

Gnomad FIN AF: 0.232

Gnomad MID AF: 0.242

Gnomad NFE AF: 0.149

Gnomad OTH AF: 0.179

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

GnomAD4 genome AF: 0.167 AC: 25349 AN: 151940 Hom.: 2235 Cov.: 32 AF XY: 0.173 AC XY: 12839 AN XY: 74250

Gnomad4 AFR AF: 0.174

Gnomad4 AMR AF: 0.224

Gnomad4 ASJ AF: 0.140

Gnomad4 EAS AF: 0.0804

Gnomad4 SAS AF: 0.116

Gnomad4 FIN AF: 0.232

Gnomad4 NFE AF: 0.149

Gnomad4 OTH AF: 0.178

Alfa AF: 0.150 Hom.: 476

Bravo AF: 0.168

Asia WGS AF: 0.0970 AC: 339 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	0.69
DANN	Benign	0.21

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6890673; hg19: chr5-161831821;