11-128455658-T-C

Position:

• chr11-128455658-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 0.443 in 151,986 control chromosomes in the GnomAD database, including 16,113 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 0.44 (16113 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.265

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.547 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.128455658T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.444 AC: 67361 AN: 151868 Hom.: 16113 Cov.: 32

Gnomad AFR AF: 0.259

Gnomad AMI AF: 0.499

Gnomad AMR AF: 0.411

Gnomad ASJ AF: 0.575

Gnomad EAS AF: 0.564

Gnomad SAS AF: 0.553

Gnomad FIN AF: 0.586

Gnomad MID AF: 0.601

Gnomad NFE AF: 0.515

Gnomad OTH AF: 0.467

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

GnomAD4 genome AF: 0.443 AC: 67365 AN: 151986 Hom.: 16113 Cov.: 32 AF XY: 0.448 AC XY: 33246 AN XY: 74274

Gnomad4 AFR AF: 0.259

Gnomad4 AMR AF: 0.410

Gnomad4 ASJ AF: 0.575

Gnomad4 EAS AF: 0.564

Gnomad4 SAS AF: 0.552

Gnomad4 FIN AF: 0.586

Gnomad4 NFE AF: 0.515

Gnomad4 OTH AF: 0.473

Alfa AF: 0.497 Hom.: 25885

Bravo AF: 0.423

Asia WGS AF: 0.574 AC: 1995 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	5.0
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10893872; hg19: chr11-128325553;