11-4548605-C-T

Position:

• chr11-4548605-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 0.354 in 152,022 control chromosomes in the GnomAD database, including 9,630 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 0.35 (9630 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.44

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.439 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.354 AC: 53777 AN: 151902 Hom.: 9625 Cov.: 32

Gnomad AFR AF: 0.331

Gnomad AMI AF: 0.407

Gnomad AMR AF: 0.272

Gnomad ASJ AF: 0.447

Gnomad EAS AF: 0.289

Gnomad SAS AF: 0.455

Gnomad FIN AF: 0.377

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.375

Gnomad OTH AF: 0.356

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

GnomAD4 genome AF: 0.354 AC: 53800 AN: 152022 Hom.: 9630 Cov.: 32 AF XY: 0.353 AC XY: 26264 AN XY: 74306

Gnomad4 AFR AF: 0.331

Gnomad4 AMR AF: 0.271

Gnomad4 ASJ AF: 0.447

Gnomad4 EAS AF: 0.289

Gnomad4 SAS AF: 0.455

Gnomad4 FIN AF: 0.377

Gnomad4 NFE AF: 0.375

Gnomad4 OTH AF: 0.357

Alfa AF: 0.234 Hom.: 516

Bravo AF: 0.345

Asia WGS AF: 0.361 AC: 1255 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.25
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1430397; hg19: chr11-4569835;