rs524386

Positions:

• chr11-64817487-T-C

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;