5-175448999-G-A

Variant names:

• chr5-175448999-G-A
• rs2168631

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 0.216 in 151,854 control chromosomes in the GnomAD database, including 3,795 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 (3795 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.200
• Publications: 15 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.376 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: 0.216 AC: 32715 AN: 151738 Hom.: 3794 Cov.: 32

Gnomad AFR AF: 0.267

Gnomad AMI AF: 0.105

Gnomad AMR AF: 0.243

Gnomad ASJ AF: 0.257

Gnomad EAS AF: 0.391

Gnomad SAS AF: 0.267

Gnomad FIN AF: 0.167

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.167

Gnomad OTH AF: 0.226

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

GnomAD4 genome AF: 0.216 AC: 32730 AN: 151854 Hom.: 3795 Cov.: 32 AF XY: 0.217 AC XY: 16141 AN XY: 74218

African (AFR) AF: 0.267 AC: 11056 AN: 41396

American (AMR) AF: 0.243 AC: 3699 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.257 AC: 892 AN: 3466

East Asian (EAS) AF: 0.390 AC: 2019 AN: 5178

South Asian (SAS) AF: 0.267 AC: 1286 AN: 4822

European-Finnish (FIN) AF: 0.167 AC: 1760 AN: 10508

Middle Eastern (MID) AF: 0.306 AC: 90 AN: 294

European-Non Finnish (NFE) AF: 0.167 AC: 11354 AN: 67936

Other (OTH) AF: 0.227 AC: 478 AN: 2108

Alfa AF: 0.198 Hom.: 5402

Bravo AF: 0.228

Asia WGS AF: 0.307 AC: 1068 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.6
DANN	Benign	0.75
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs2168631; hg19: chr5-174876002;