rs524386

Variant names:

• chr11-64817487-T-C
• rs524386

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 0.0985 in 151,858 control chromosomes in the GnomAD database, including 1,192 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 0.099 (1192 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.400
• Publications: 13 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.329 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: 0.0985 AC: 14949 AN: 151740 Hom.: 1195 Cov.: 30

Gnomad AFR AF: 0.0202

Gnomad AMI AF: 0.0451

Gnomad AMR AF: 0.220

Gnomad ASJ AF: 0.113

Gnomad EAS AF: 0.341

Gnomad SAS AF: 0.159

Gnomad FIN AF: 0.124

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0926

Gnomad OTH AF: 0.0939

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

GnomAD4 genome AF: 0.0985 AC: 14959 AN: 151858 Hom.: 1192 Cov.: 30 AF XY: 0.106 AC XY: 7835 AN XY: 74194

African (AFR) AF: 0.0201 AC: 832 AN: 41410

American (AMR) AF: 0.220 AC: 3336 AN: 15170

Ashkenazi Jewish (ASJ) AF: 0.113 AC: 390 AN: 3466

East Asian (EAS) AF: 0.342 AC: 1770 AN: 5178

South Asian (SAS) AF: 0.159 AC: 765 AN: 4798

European-Finnish (FIN) AF: 0.124 AC: 1313 AN: 10552

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0926 AC: 6294 AN: 67970

Other (OTH) AF: 0.0962 AC: 203 AN: 2110

Alfa AF: 0.0996 Hom.: 1824

Bravo AF: 0.104

Asia WGS AF: 0.253 AC: 879 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.3
DANN	Benign	0.45
PhyloP100		-0.40

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs524386; hg19: chr11-64584959;