11-1149193-C-T

Variant names:

• chr11-1149193-C-T
• rs9667239

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 0.138 in 152,256 control chromosomes in the GnomAD database, including 1,575 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 0.14 (1575 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.22
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.174 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: 0.138 AC: 20955 AN: 152138 Hom.: 1569 Cov.: 33

Gnomad AFR AF: 0.178

Gnomad AMI AF: 0.140

Gnomad AMR AF: 0.105

Gnomad ASJ AF: 0.0786

Gnomad EAS AF: 0.00424

Gnomad SAS AF: 0.0683

Gnomad FIN AF: 0.222

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.126

Gnomad OTH AF: 0.125

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

GnomAD4 genome AF: 0.138 AC: 20962 AN: 152256 Hom.: 1575 Cov.: 33 AF XY: 0.139 AC XY: 10361 AN XY: 74458

African (AFR) AF: 0.178 AC: 7376 AN: 41542

American (AMR) AF: 0.105 AC: 1610 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0786 AC: 273 AN: 3472

East Asian (EAS) AF: 0.00425 AC: 22 AN: 5174

South Asian (SAS) AF: 0.0683 AC: 330 AN: 4830

European-Finnish (FIN) AF: 0.222 AC: 2352 AN: 10614

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.126 AC: 8580 AN: 68002

Other (OTH) AF: 0.125 AC: 263 AN: 2112

Alfa AF: 0.128 Hom.: 144

Bravo AF: 0.131

Asia WGS AF: 0.0430 AC: 149 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.083
DANN	Benign	0.71
PhyloP100		-4.2

Splicing

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

Other links and lift over

dbSNP: rs9667239; hg19: chr11-1143101;