11-612355-T-C

Position:

• chr11-612355-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 0.268 in 515,928 control chromosomes in the GnomAD database, including 22,124 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 0.33 (9417 hom., cov: 34)
  • Exomes 𝑓: 0.24 (12707 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.975

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 (AFR) allele frequency at 95% confidence interval = 0.513 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: 0.325 AC: 49422 AN: 152054 Hom.: 9401 Cov.: 34

Gnomad AFR AF: 0.519

Gnomad AMI AF: 0.208

Gnomad AMR AF: 0.306

Gnomad ASJ AF: 0.347

Gnomad EAS AF: 0.0255

Gnomad SAS AF: 0.128

Gnomad FIN AF: 0.185

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.270

Gnomad OTH AF: 0.331

GnomAD4 exome AF: 0.243 AC: 88573 AN: 363756 Hom.: 12707 AF XY: 0.237 AC XY: 44950 AN XY: 189322

Gnomad4 AFR exome AF: 0.515

Gnomad4 AMR exome AF: 0.307

Gnomad4 ASJ exome AF: 0.329

Gnomad4 EAS exome AF: 0.0213

Gnomad4 SAS exome AF: 0.134

Gnomad4 FIN exome AF: 0.201

Gnomad4 NFE exome AF: 0.267

Gnomad4 OTH exome AF: 0.268

GnomAD4 genome AF: 0.325 AC: 49473 AN: 152172 Hom.: 9417 Cov.: 34 AF XY: 0.314 AC XY: 23369 AN XY: 74398

Gnomad4 AFR AF: 0.519

Gnomad4 AMR AF: 0.307

Gnomad4 ASJ AF: 0.347

Gnomad4 EAS AF: 0.0255

Gnomad4 SAS AF: 0.127

Gnomad4 FIN AF: 0.185

Gnomad4 NFE AF: 0.270

Gnomad4 OTH AF: 0.330

Alfa AF: 0.275 Hom.: 5735

Bravo AF: 0.346

Asia WGS AF: 0.126 AC: 439 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	1.3
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: rs12805435; hg19: chr11-612355;