chr11-80666008-C-T

Variant names:

• chr11-80666008-C-T
• rs17140547

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 0.0268 in 152,188 control chromosomes in the GnomAD database, including 197 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 0.027 (197 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.468
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.58).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.225 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: 0.0269 AC: 4087 AN: 152072 Hom.: 201 Cov.: 32

Gnomad AFR AF: 0.0270

Gnomad AMI AF: 0.0143

Gnomad AMR AF: 0.0194

Gnomad ASJ AF: 0.0179

Gnomad EAS AF: 0.237

Gnomad SAS AF: 0.0788

Gnomad FIN AF: 0.00801

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0124

Gnomad OTH AF: 0.0249

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

GnomAD4 genome AF: 0.0268 AC: 4078 AN: 152188 Hom.: 197 Cov.: 32 AF XY: 0.0278 AC XY: 2070 AN XY: 74388

African (AFR) AF: 0.0270 AC: 1123 AN: 41528

American (AMR) AF: 0.0193 AC: 295 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0179 AC: 62 AN: 3470

East Asian (EAS) AF: 0.236 AC: 1220 AN: 5162

South Asian (SAS) AF: 0.0782 AC: 377 AN: 4820

European-Finnish (FIN) AF: 0.00801 AC: 85 AN: 10606

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.0124 AC: 844 AN: 68010

Other (OTH) AF: 0.0237 AC: 50 AN: 2110

Alfa AF: 0.0218 Hom.: 230

Bravo AF: 0.0289

Asia WGS AF: 0.133 AC: 462 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.58
CADD	Benign	15
DANN	Benign	0.84
PhyloP100		0.47

Splicing

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

Other links and lift over

dbSNP: rs17140547; hg19: chr11-80377052;