5-180599672-C-G

Variant names:

• chr5-180599672-C-G
• rs10055319

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 0.225 in 152,054 control chromosomes in the GnomAD database, including 4,421 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 0.22 (4421 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.365
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.457 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.225 AC: 34120 AN: 151936 Hom.: 4400 Cov.: 32

Gnomad AFR AF: 0.304

Gnomad AMI AF: 0.0791

Gnomad AMR AF: 0.175

Gnomad ASJ AF: 0.354

Gnomad EAS AF: 0.472

Gnomad SAS AF: 0.305

Gnomad FIN AF: 0.148

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.170

Gnomad OTH AF: 0.236

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

GnomAD4 genome AF: 0.225 AC: 34171 AN: 152054 Hom.: 4421 Cov.: 32 AF XY: 0.226 AC XY: 16780 AN XY: 74334

African (AFR) AF: 0.304 AC: 12620 AN: 41492

American (AMR) AF: 0.175 AC: 2673 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.354 AC: 1229 AN: 3472

East Asian (EAS) AF: 0.473 AC: 2431 AN: 5144

South Asian (SAS) AF: 0.303 AC: 1455 AN: 4806

European-Finnish (FIN) AF: 0.148 AC: 1568 AN: 10596

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.170 AC: 11528 AN: 67946

Other (OTH) AF: 0.244 AC: 514 AN: 2108

Alfa AF: 0.185 Hom.: 408

Bravo AF: 0.233

Asia WGS AF: 0.383 AC: 1335 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.4
DANN	Benign	0.65
PhyloP100		0.36

Splicing

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

Other links and lift over

dbSNP: rs10055319; hg19: chr5-180026672;