rs11826261

Variant names:

• chr11-58747690-C-T
• rs11826261

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 0.0348 in 152,108 control chromosomes in the GnomAD database, including 132 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 0.035 (132 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.42
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0744 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: 0.0348 AC: 5290 AN: 151990 Hom.: 132 Cov.: 32

Gnomad AFR AF: 0.0766

Gnomad AMI AF: 0.0175

Gnomad AMR AF: 0.0159

Gnomad ASJ AF: 0.0297

Gnomad EAS AF: 0.0357

Gnomad SAS AF: 0.0461

Gnomad FIN AF: 0.00340

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0185

Gnomad OTH AF: 0.0259

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

GnomAD4 genome AF: 0.0348 AC: 5297 AN: 152108 Hom.: 132 Cov.: 32 AF XY: 0.0340 AC XY: 2530 AN XY: 74340

African (AFR) AF: 0.0766 AC: 3177 AN: 41480

American (AMR) AF: 0.0159 AC: 242 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.0297 AC: 103 AN: 3468

East Asian (EAS) AF: 0.0354 AC: 183 AN: 5176

South Asian (SAS) AF: 0.0457 AC: 220 AN: 4814

European-Finnish (FIN) AF: 0.00340 AC: 36 AN: 10586

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

European-Non Finnish (NFE) AF: 0.0185 AC: 1255 AN: 68000

Other (OTH) AF: 0.0265 AC: 56 AN: 2110

Alfa AF: 0.0270 Hom.: 124

Bravo AF: 0.0385

Asia WGS AF: 0.0460 AC: 163 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.34
DANN	Benign	0.38
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs11826261; hg19: chr11-58515163;