rs524386

Variant names:

• chr11-64817487-T-C
• rs524386

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.0201

Gnomad4 AMR AF: 0.220

Gnomad4 ASJ AF: 0.113

Gnomad4 EAS AF: 0.342

Gnomad4 SAS AF: 0.159

Gnomad4 FIN AF: 0.124

Gnomad4 NFE AF: 0.0926

Gnomad4 OTH AF: 0.0962

Alfa AF: 0.0965 Hom.: 1224

Bravo AF: 0.104

Asia WGS AF: 0.253 AC: 879 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs524386; hg19: chr11-64584959;