11-4593436-C-T

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 0.593 in 175,726 control chromosomes in the GnomAD database, including 31,173 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 0.59 (26910 hom., cov: 33)
  • Exomes 𝑓: 0.59 (4263 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.160

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.638 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: 0.594 AC: 90223 AN: 151930 Hom.: 26883 Cov.: 33

Gnomad AFR AF: 0.528

Gnomad AMI AF: 0.428

Gnomad AMR AF: 0.648

Gnomad ASJ AF: 0.584

Gnomad EAS AF: 0.582

Gnomad SAS AF: 0.610

Gnomad FIN AF: 0.621

Gnomad MID AF: 0.642

Gnomad NFE AF: 0.618

Gnomad OTH AF: 0.620

GnomAD4 exome AF: 0.591 AC: 13993 AN: 23678 Hom.: 4263 Cov.: 0 AF XY: 0.591 AC XY: 7391 AN XY: 12508

Gnomad4 AFR exome AF: 0.482

Gnomad4 AMR exome AF: 0.634

Gnomad4 ASJ exome AF: 0.541

Gnomad4 EAS exome AF: 0.587

Gnomad4 SAS exome AF: 0.604

Gnomad4 FIN exome AF: 0.569

Gnomad4 NFE exome AF: 0.586

Gnomad4 OTH exome AF: 0.574

GnomAD4 genome AF: 0.594 AC: 90294 AN: 152048 Hom.: 26910 Cov.: 33 AF XY: 0.597 AC XY: 44390 AN XY: 74330

Gnomad4 AFR AF: 0.529

Gnomad4 AMR AF: 0.648

Gnomad4 ASJ AF: 0.584

Gnomad4 EAS AF: 0.583

Gnomad4 SAS AF: 0.609

Gnomad4 FIN AF: 0.621

Gnomad4 NFE AF: 0.618

Gnomad4 OTH AF: 0.617

Alfa AF: 0.602 Hom.: 3372

Bravo AF: 0.590

Asia WGS AF: 0.597 AC: 2074 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	1.3
Dann	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1505204; hg19: chr11-4614666;