chr5-175449424-A-T

Variant names:

• chr5-175449424-A-T
• rs6882300

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 0.0712 in 152,196 control chromosomes in the GnomAD database, including 748 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 0.071 (748 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.703
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.191 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: 0.0712 AC: 10832 AN: 152078 Hom.: 746 Cov.: 33

Gnomad AFR AF: 0.169

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0506

Gnomad ASJ AF: 0.0248

Gnomad EAS AF: 0.202

Gnomad SAS AF: 0.114

Gnomad FIN AF: 0.0193

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0154

Gnomad OTH AF: 0.0627

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

GnomAD4 genome AF: 0.0712 AC: 10843 AN: 152196 Hom.: 748 Cov.: 33 AF XY: 0.0712 AC XY: 5295 AN XY: 74418

African (AFR) AF: 0.169 AC: 6997 AN: 41488

American (AMR) AF: 0.0504 AC: 771 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0248 AC: 86 AN: 3470

East Asian (EAS) AF: 0.201 AC: 1044 AN: 5182

South Asian (SAS) AF: 0.113 AC: 545 AN: 4830

European-Finnish (FIN) AF: 0.0193 AC: 205 AN: 10602

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.0154 AC: 1047 AN: 68018

Other (OTH) AF: 0.0649 AC: 137 AN: 2112

Alfa AF: 0.0480 Hom.: 55

Bravo AF: 0.0787

Asia WGS AF: 0.169 AC: 588 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	7.3
DANN	Benign	0.79
PhyloP100		0.70

Splicing

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

Other links and lift over

dbSNP: rs6882300; hg19: chr5-174876427;