11-116169550-G-C

Variant names:

• chr11-116169550-G-C
• rs1961328

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 0.507 in 152,096 control chromosomes in the GnomAD database, including 19,962 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 0.51 (19962 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.913
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.643 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: 0.507 AC: 77031 AN: 151978 Hom.: 19956 Cov.: 33

Gnomad AFR AF: 0.419

Gnomad AMI AF: 0.563

Gnomad AMR AF: 0.434

Gnomad ASJ AF: 0.480

Gnomad EAS AF: 0.612

Gnomad SAS AF: 0.661

Gnomad FIN AF: 0.499

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.560

Gnomad OTH AF: 0.499

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

GnomAD4 genome AF: 0.507 AC: 77059 AN: 152096 Hom.: 19962 Cov.: 33 AF XY: 0.507 AC XY: 37678 AN XY: 74338

African (AFR) AF: 0.419 AC: 17372 AN: 41500

American (AMR) AF: 0.434 AC: 6636 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.480 AC: 1666 AN: 3470

East Asian (EAS) AF: 0.611 AC: 3159 AN: 5166

South Asian (SAS) AF: 0.662 AC: 3192 AN: 4824

European-Finnish (FIN) AF: 0.499 AC: 5275 AN: 10564

Middle Eastern (MID) AF: 0.408 AC: 120 AN: 294

European-Non Finnish (NFE) AF: 0.560 AC: 38069 AN: 67964

Other (OTH) AF: 0.500 AC: 1057 AN: 2116

Alfa AF: 0.339 Hom.: 774

Bravo AF: 0.494

Asia WGS AF: 0.626 AC: 2175 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	9.3
DANN	Benign	0.57
PhyloP100		0.91

Splicing

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

Other links and lift over

dbSNP: rs1961328; hg19: chr11-116040267;