11-4548605-C-T

Variant names:

• chr11-4548605-C-T
• rs1430397

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.331 AC: 13707 AN: 41452

American (AMR) AF: 0.271 AC: 4147 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.447 AC: 1550 AN: 3470

East Asian (EAS) AF: 0.289 AC: 1494 AN: 5162

South Asian (SAS) AF: 0.455 AC: 2194 AN: 4822

European-Finnish (FIN) AF: 0.377 AC: 3975 AN: 10550

Middle Eastern (MID) AF: 0.333 AC: 98 AN: 294

European-Non Finnish (NFE) AF: 0.375 AC: 25512 AN: 67972

Other (OTH) AF: 0.357 AC: 752 AN: 2106

Alfa AF: 0.238 Hom.: 552

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
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs1430397; hg19: chr11-4569835;