chr5-178667483-A-G

Variant names:

• chr5-178667483-A-G
• rs10516147

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.206 in 152,130 control chromosomes in the GnomAD database, including 3,832 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 0.21 (3832 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.58
• Publications: 14 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.361 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.206 AC: 31271 AN: 152012 Hom.: 3832 Cov.: 32

Gnomad AFR AF: 0.0785

Gnomad AMI AF: 0.192

Gnomad AMR AF: 0.238

Gnomad ASJ AF: 0.187

Gnomad EAS AF: 0.375

Gnomad SAS AF: 0.335

Gnomad FIN AF: 0.358

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.232

Gnomad OTH AF: 0.199

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

GnomAD4 genome AF: 0.206 AC: 31281 AN: 152130 Hom.: 3832 Cov.: 32 AF XY: 0.215 AC XY: 15991 AN XY: 74338

African (AFR) AF: 0.0784 AC: 3255 AN: 41536

American (AMR) AF: 0.237 AC: 3628 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.187 AC: 650 AN: 3472

East Asian (EAS) AF: 0.375 AC: 1940 AN: 5178

South Asian (SAS) AF: 0.336 AC: 1620 AN: 4820

European-Finnish (FIN) AF: 0.358 AC: 3777 AN: 10562

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.232 AC: 15743 AN: 67976

Other (OTH) AF: 0.204 AC: 429 AN: 2104

Alfa AF: 0.212 Hom.: 7170

Bravo AF: 0.186

Asia WGS AF: 0.370 AC: 1290 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.88
DANN	Benign	0.28
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs10516147; hg19: chr5-178094484; COSMIC: COSV60238739;