rs11245788

Variant names:

• chr11-50154550-C-G
• rs11245788

Your query was ambiguous. Multiple possible variants found:

• chr11-50154550-C-G
• chr11-50154550-C-T

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 0.354 in 151,774 control chromosomes in the GnomAD database, including 11,741 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 0.35 (11741 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.556
• Publications: 1 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 (AMR) allele frequency at 95% confidence interval = 0.499 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: 0.354 AC: 53638 AN: 151656 Hom.: 11732 Cov.: 32

Gnomad AFR AF: 0.0894

Gnomad AMI AF: 0.570

Gnomad AMR AF: 0.509

Gnomad ASJ AF: 0.565

Gnomad EAS AF: 0.319

Gnomad SAS AF: 0.298

Gnomad FIN AF: 0.469

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.453

Gnomad OTH AF: 0.413

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

GnomAD4 genome AF: 0.354 AC: 53660 AN: 151774 Hom.: 11741 Cov.: 32 AF XY: 0.355 AC XY: 26360 AN XY: 74172

African (AFR) AF: 0.0891 AC: 3692 AN: 41434

American (AMR) AF: 0.509 AC: 7754 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.565 AC: 1958 AN: 3466

East Asian (EAS) AF: 0.319 AC: 1641 AN: 5150

South Asian (SAS) AF: 0.300 AC: 1439 AN: 4800

European-Finnish (FIN) AF: 0.469 AC: 4929 AN: 10514

Middle Eastern (MID) AF: 0.455 AC: 133 AN: 292

European-Non Finnish (NFE) AF: 0.453 AC: 30715 AN: 67856

Other (OTH) AF: 0.417 AC: 880 AN: 2108

Alfa AF: 0.398 Hom.: 1686

Bravo AF: 0.349

Asia WGS AF: 0.299 AC: 1039 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	0.36
DANN	Benign	0.38
PhyloP100		0.56

Splicing

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

Other links and lift over

dbSNP: rs11245788; hg19: chr11-50113721;