5-175437204-A-G

Variant names:

• chr5-175437204-A-G
• rs11747886

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 0.182 in 151,448 control chromosomes in the GnomAD database, including 2,709 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 0.18 (2709 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.26
• Publications: 3 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 (AFR) allele frequency at 95% confidence interval = 0.241 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.182 AC: 27513 AN: 151332 Hom.: 2707 Cov.: 32

Gnomad AFR AF: 0.245

Gnomad AMI AF: 0.111

Gnomad AMR AF: 0.202

Gnomad ASJ AF: 0.195

Gnomad EAS AF: 0.188

Gnomad SAS AF: 0.123

Gnomad FIN AF: 0.150

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.148

Gnomad OTH AF: 0.185

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

GnomAD4 genome AF: 0.182 AC: 27521 AN: 151448 Hom.: 2709 Cov.: 32 AF XY: 0.181 AC XY: 13383 AN XY: 73992

African (AFR) AF: 0.245 AC: 10083 AN: 41236

American (AMR) AF: 0.202 AC: 3075 AN: 15222

Ashkenazi Jewish (ASJ) AF: 0.195 AC: 676 AN: 3458

East Asian (EAS) AF: 0.188 AC: 965 AN: 5146

South Asian (SAS) AF: 0.123 AC: 585 AN: 4766

European-Finnish (FIN) AF: 0.150 AC: 1570 AN: 10496

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.148 AC: 10009 AN: 67822

Other (OTH) AF: 0.184 AC: 385 AN: 2096

Alfa AF: 0.165 Hom.: 334

Bravo AF: 0.192

Asia WGS AF: 0.135 AC: 469 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	0.23
DANN	Benign	0.49
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs11747886; hg19: chr5-174864207;