11-13150399-C-T

Variant names:

• chr11-13150399-C-T
• rs11022693

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 0.203 in 152,128 control chromosomes in the GnomAD database, including 3,845 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 0.20 (3845 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.261
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.278 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: 0.203 AC: 30812 AN: 152010 Hom.: 3839 Cov.: 32

Gnomad AFR AF: 0.0511

Gnomad AMI AF: 0.181

Gnomad AMR AF: 0.235

Gnomad ASJ AF: 0.282

Gnomad EAS AF: 0.138

Gnomad SAS AF: 0.187

Gnomad FIN AF: 0.254

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.281

Gnomad OTH AF: 0.226

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

GnomAD4 genome AF: 0.203 AC: 30830 AN: 152128 Hom.: 3845 Cov.: 32 AF XY: 0.202 AC XY: 14986 AN XY: 74348

African (AFR) AF: 0.0509 AC: 2114 AN: 41524

American (AMR) AF: 0.235 AC: 3589 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.282 AC: 978 AN: 3468

East Asian (EAS) AF: 0.138 AC: 715 AN: 5164

South Asian (SAS) AF: 0.188 AC: 905 AN: 4820

European-Finnish (FIN) AF: 0.254 AC: 2687 AN: 10580

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.281 AC: 19132 AN: 67978

Other (OTH) AF: 0.228 AC: 482 AN: 2112

Alfa AF: 0.252 Hom.: 15365

Bravo AF: 0.195

Asia WGS AF: 0.149 AC: 518 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.5
DANN	Benign	0.49
PhyloP100		-0.26

Splicing

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

Other links and lift over

dbSNP: rs11022693; hg19: chr11-13171946;