rs11952171

chr5-174268775-A-G

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.225

Gnomad4 AMR AF: 0.202

Gnomad4 ASJ AF: 0.169

Gnomad4 EAS AF: 0.0487

Gnomad4 SAS AF: 0.187

Gnomad4 FIN AF: 0.244

Gnomad4 NFE AF: 0.195

Gnomad4 OTH AF: 0.195

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11952171; hg19: chr5-173695778;