rs11952171

Variant names:

• chr5-174268775-A-G
• rs11952171

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 0.201 in 152,038 control chromosomes in the GnomAD database, including 3,166 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 0.20 (3166 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.218
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.221 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.201 AC: 30596 AN: 151918 Hom.: 3164 Cov.: 30

Gnomad AFR AF: 0.225

Gnomad AMI AF: 0.143

Gnomad AMR AF: 0.202

Gnomad ASJ AF: 0.169

Gnomad EAS AF: 0.0486

Gnomad SAS AF: 0.187

Gnomad FIN AF: 0.244

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.195

Gnomad OTH AF: 0.197

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

GnomAD4 genome AF: 0.201 AC: 30613 AN: 152038 Hom.: 3166 Cov.: 30 AF XY: 0.203 AC XY: 15083 AN XY: 74340

African (AFR) AF: 0.225 AC: 9326 AN: 41488

American (AMR) AF: 0.202 AC: 3080 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.169 AC: 588 AN: 3472

East Asian (EAS) AF: 0.0487 AC: 252 AN: 5172

South Asian (SAS) AF: 0.187 AC: 901 AN: 4818

European-Finnish (FIN) AF: 0.244 AC: 2584 AN: 10586

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.195 AC: 13277 AN: 67932

Other (OTH) AF: 0.195 AC: 412 AN: 2112

Alfa AF: 0.205 Hom.: 410

Bravo AF: 0.198

Asia WGS AF: 0.147 AC: 515 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	9.5
DANN	Benign	0.94
PhyloP100		0.22

Splicing

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

Other links and lift over

dbSNP: rs11952171; hg19: chr5-173695778;