rs174468

Variant names:

• chr11-61896219-G-A
• rs174468

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 0.284 in 152,064 control chromosomes in the GnomAD database, including 8,002 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 0.28 (8002 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00200

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.413 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: 0.284 AC: 43170 AN: 151948 Hom.: 8003 Cov.: 33

Gnomad AFR AF: 0.0785

Gnomad AMI AF: 0.499

Gnomad AMR AF: 0.264

Gnomad ASJ AF: 0.459

Gnomad EAS AF: 0.0234

Gnomad SAS AF: 0.220

Gnomad FIN AF: 0.334

Gnomad MID AF: 0.395

Gnomad NFE AF: 0.417

Gnomad OTH AF: 0.313

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

GnomAD4 genome AF: 0.284 AC: 43164 AN: 152064 Hom.: 8002 Cov.: 33 AF XY: 0.278 AC XY: 20655 AN XY: 74330

Gnomad4 AFR AF: 0.0783

Gnomad4 AMR AF: 0.264

Gnomad4 ASJ AF: 0.459

Gnomad4 EAS AF: 0.0234

Gnomad4 SAS AF: 0.221

Gnomad4 FIN AF: 0.334

Gnomad4 NFE AF: 0.417

Gnomad4 OTH AF: 0.313

Alfa AF: 0.390 Hom.: 8554

Bravo AF: 0.270

Asia WGS AF: 0.153 AC: 535 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.0
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs174468; hg19: chr11-61663691;