chr5-166165005-G-C

Variant names:

• chr5-166165005-G-C
• rs9313310

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 0.0545 in 152,240 control chromosomes in the GnomAD database, including 456 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 0.055 (456 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.112 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: 0.0544 AC: 8274 AN: 152122 Hom.: 452 Cov.: 32

Gnomad AFR AF: 0.109

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.116

Gnomad ASJ AF: 0.00980

Gnomad EAS AF: 0.118

Gnomad SAS AF: 0.0222

Gnomad FIN AF: 0.00613

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0156

Gnomad OTH AF: 0.0454

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

GnomAD4 genome AF: 0.0545 AC: 8301 AN: 152240 Hom.: 456 Cov.: 32 AF XY: 0.0556 AC XY: 4136 AN XY: 74444

African (AFR) AF: 0.109 AC: 4538 AN: 41536

American (AMR) AF: 0.116 AC: 1777 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.00980 AC: 34 AN: 3470

East Asian (EAS) AF: 0.119 AC: 614 AN: 5162

South Asian (SAS) AF: 0.0224 AC: 108 AN: 4826

European-Finnish (FIN) AF: 0.00613 AC: 65 AN: 10612

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.0156 AC: 1061 AN: 68014

Other (OTH) AF: 0.0464 AC: 98 AN: 2114

Alfa AF: 0.0115 Hom.: 7

Bravo AF: 0.0653

Asia WGS AF: 0.0760 AC: 263 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.087
DANN	Benign	0.41
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs9313310; hg19: chr5-165592010;