chr11-61896219-G-A

Variant names:

• chr11-61896219-G-A
• rs174468

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 0.284 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
• Publications: 38 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

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: 0.284 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

African (AFR) AF: 0.0783 AC: 3251 AN: 41522

American (AMR) AF: 0.264 AC: 4032 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.459 AC: 1592 AN: 3470

East Asian (EAS) AF: 0.0234 AC: 121 AN: 5168

South Asian (SAS) AF: 0.221 AC: 1060 AN: 4798

European-Finnish (FIN) AF: 0.334 AC: 3533 AN: 10590

Middle Eastern (MID) AF: 0.394 AC: 115 AN: 292

European-Non Finnish (NFE) AF: 0.417 AC: 28349 AN: 67930

Other (OTH) AF: 0.313 AC: 660 AN: 2108

Alfa AF: 0.349 Hom.: 14287

Bravo AF: 0.270

Asia WGS AF: 0.153 AC: 535 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.0
DANN	Benign	0.43
PhyloP100		-0.0020

Splicing

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

Other links and lift over

dbSNP: rs174468; hg19: chr11-61663691;