11-38717823-A-G

Variant names:

• chr11-38717823-A-G
• rs1504233

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 0.921 in 152,106 control chromosomes in the GnomAD database, including 65,351 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 0.92 (65351 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.146
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.987 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.921 AC: 140056 AN: 151988 Hom.: 65327 Cov.: 33

Gnomad AFR AF: 0.767

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.960

Gnomad ASJ AF: 0.978

Gnomad EAS AF: 0.896

Gnomad SAS AF: 0.923

Gnomad FIN AF: 0.988

Gnomad MID AF: 0.959

Gnomad NFE AF: 0.993

Gnomad OTH AF: 0.949

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

GnomAD4 genome AF: 0.921 AC: 140127 AN: 152106 Hom.: 65351 Cov.: 33 AF XY: 0.922 AC XY: 68534 AN XY: 74354

African (AFR) AF: 0.766 AC: 31768 AN: 41464

American (AMR) AF: 0.960 AC: 14643 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.978 AC: 3397 AN: 3472

East Asian (EAS) AF: 0.896 AC: 4613 AN: 5150

South Asian (SAS) AF: 0.924 AC: 4453 AN: 4818

European-Finnish (FIN) AF: 0.988 AC: 10488 AN: 10620

Middle Eastern (MID) AF: 0.949 AC: 279 AN: 294

European-Non Finnish (NFE) AF: 0.993 AC: 67569 AN: 68012

Other (OTH) AF: 0.949 AC: 2005 AN: 2112

Alfa AF: 0.924 Hom.: 9176

Bravo AF: 0.914

Asia WGS AF: 0.912 AC: 3168 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.9
DANN	Benign	0.51
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs1504233; hg19: chr11-38739373;