11-64382898-T-C

Variant names:

• chr11-64382898-T-C
• rs559928

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 0.777 in 152,098 control chromosomes in the GnomAD database, including 46,598 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 0.78 (46598 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0860

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.887 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: 0.777 AC: 118100 AN: 151980 Hom.: 46576 Cov.: 31

Gnomad AFR AF: 0.632

Gnomad AMI AF: 0.842

Gnomad AMR AF: 0.857

Gnomad ASJ AF: 0.897

Gnomad EAS AF: 0.887

Gnomad SAS AF: 0.909

Gnomad FIN AF: 0.802

Gnomad MID AF: 0.889

Gnomad NFE AF: 0.817

Gnomad OTH AF: 0.823

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

GnomAD4 genome AF: 0.777 AC: 118171 AN: 152098 Hom.: 46598 Cov.: 31 AF XY: 0.781 AC XY: 58109 AN XY: 74372

Gnomad4 AFR AF: 0.632

Gnomad4 AMR AF: 0.857

Gnomad4 ASJ AF: 0.897

Gnomad4 EAS AF: 0.886

Gnomad4 SAS AF: 0.909

Gnomad4 FIN AF: 0.802

Gnomad4 NFE AF: 0.817

Gnomad4 OTH AF: 0.825

Alfa AF: 0.823 Hom.: 104333

Bravo AF: 0.774

Asia WGS AF: 0.883 AC: 3072 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.7
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs559928; hg19: chr11-64150370;