chr11-55576006-T-C

Variant names:

• chr11-55576006-T-C
• rs667240

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 0.242 in 152,136 control chromosomes in the GnomAD database, including 4,992 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 0.24 (4992 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0770
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.348 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: 0.242 AC: 36813 AN: 152018 Hom.: 4976 Cov.: 33

Gnomad AFR AF: 0.138

Gnomad AMI AF: 0.297

Gnomad AMR AF: 0.331

Gnomad ASJ AF: 0.240

Gnomad EAS AF: 0.362

Gnomad SAS AF: 0.247

Gnomad FIN AF: 0.322

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.262

Gnomad OTH AF: 0.273

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

GnomAD4 genome AF: 0.242 AC: 36846 AN: 152136 Hom.: 4992 Cov.: 33 AF XY: 0.245 AC XY: 18229 AN XY: 74336

African (AFR) AF: 0.138 AC: 5732 AN: 41532

American (AMR) AF: 0.332 AC: 5066 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.240 AC: 834 AN: 3468

East Asian (EAS) AF: 0.362 AC: 1864 AN: 5148

South Asian (SAS) AF: 0.248 AC: 1196 AN: 4822

European-Finnish (FIN) AF: 0.322 AC: 3398 AN: 10556

Middle Eastern (MID) AF: 0.303 AC: 89 AN: 294

European-Non Finnish (NFE) AF: 0.262 AC: 17800 AN: 68012

Other (OTH) AF: 0.282 AC: 596 AN: 2116

Alfa AF: 0.242 Hom.: 618

Bravo AF: 0.243

Asia WGS AF: 0.302 AC: 1049 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	7.1
DANN	Benign	0.31
PhyloP100		0.077

Splicing

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

Other links and lift over

dbSNP: rs667240; hg19: chr11-55343482;