chr11-1111926-T-A

Variant names:

• chr11-1111926-T-A
• rs4077757

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 0.156 in 152,166 control chromosomes in the GnomAD database, including 3,004 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 0.16 (3004 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.55
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.344 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: 0.156 AC: 23749 AN: 152048 Hom.: 2997 Cov.: 33

Gnomad AFR AF: 0.349

Gnomad AMI AF: 0.0626

Gnomad AMR AF: 0.0828

Gnomad ASJ AF: 0.0407

Gnomad EAS AF: 0.0370

Gnomad SAS AF: 0.0532

Gnomad FIN AF: 0.116

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0864

Gnomad OTH AF: 0.131

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

GnomAD4 genome AF: 0.156 AC: 23785 AN: 152166 Hom.: 3004 Cov.: 33 AF XY: 0.153 AC XY: 11406 AN XY: 74398

African (AFR) AF: 0.349 AC: 14477 AN: 41484

American (AMR) AF: 0.0827 AC: 1265 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0407 AC: 141 AN: 3466

East Asian (EAS) AF: 0.0369 AC: 191 AN: 5178

South Asian (SAS) AF: 0.0524 AC: 253 AN: 4826

European-Finnish (FIN) AF: 0.116 AC: 1234 AN: 10602

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.0864 AC: 5873 AN: 67986

Other (OTH) AF: 0.129 AC: 272 AN: 2116

Alfa AF: 0.128 Hom.: 231

Bravo AF: 0.162

Asia WGS AF: 0.0810 AC: 281 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.3
DANN	Benign	0.51
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs4077757; hg19: chr11-1105834;