11-64382898-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 0.777 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/exons	MANE	UniProt

Ensembl

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