11-73973249-G-A

Variant names:

• chr11-73973249-G-A
• rs11602906

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 0.0565 in 152,268 control chromosomes in the GnomAD database, including 381 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 0.056 (381 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.87
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0765 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: 0.0565 AC: 8600 AN: 152150 Hom.: 380 Cov.: 33

Gnomad AFR AF: 0.0141

Gnomad AMI AF: 0.123

Gnomad AMR AF: 0.0286

Gnomad ASJ AF: 0.0550

Gnomad EAS AF: 0.00115

Gnomad SAS AF: 0.0458

Gnomad FIN AF: 0.154

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0782

Gnomad OTH AF: 0.0435

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

GnomAD4 genome AF: 0.0565 AC: 8598 AN: 152268 Hom.: 381 Cov.: 33 AF XY: 0.0597 AC XY: 4447 AN XY: 74440

African (AFR) AF: 0.0141 AC: 586 AN: 41562

American (AMR) AF: 0.0285 AC: 436 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0550 AC: 191 AN: 3472

East Asian (EAS) AF: 0.00116 AC: 6 AN: 5184

South Asian (SAS) AF: 0.0460 AC: 222 AN: 4824

European-Finnish (FIN) AF: 0.154 AC: 1626 AN: 10592

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.0783 AC: 5323 AN: 68016

Other (OTH) AF: 0.0431 AC: 91 AN: 2112

Alfa AF: 0.0635 Hom.: 576

Bravo AF: 0.0445

Asia WGS AF: 0.0180 AC: 64 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.51
DANN	Benign	0.47
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs11602906; hg19: chr11-73684294;