chr11-56300625-T-C

Variant names:

• chr11-56300625-T-C
• rs11227802

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 0.486 in 151,762 control chromosomes in the GnomAD database, including 18,514 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 0.49 (18514 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.144
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.704 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: 0.486 AC: 73743 AN: 151642 Hom.: 18472 Cov.: 32

Gnomad AFR AF: 0.454

Gnomad AMI AF: 0.350

Gnomad AMR AF: 0.609

Gnomad ASJ AF: 0.463

Gnomad EAS AF: 0.723

Gnomad SAS AF: 0.624

Gnomad FIN AF: 0.451

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.458

Gnomad OTH AF: 0.508

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

GnomAD4 genome AF: 0.486 AC: 73829 AN: 151762 Hom.: 18514 Cov.: 32 AF XY: 0.494 AC XY: 36629 AN XY: 74182

African (AFR) AF: 0.454 AC: 18813 AN: 41432

American (AMR) AF: 0.610 AC: 9308 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.463 AC: 1602 AN: 3462

East Asian (EAS) AF: 0.723 AC: 3739 AN: 5170

South Asian (SAS) AF: 0.623 AC: 3006 AN: 4824

European-Finnish (FIN) AF: 0.451 AC: 4761 AN: 10560

Middle Eastern (MID) AF: 0.524 AC: 154 AN: 294

European-Non Finnish (NFE) AF: 0.458 AC: 31046 AN: 67746

Other (OTH) AF: 0.513 AC: 1081 AN: 2106

Alfa AF: 0.476 Hom.: 20240

Bravo AF: 0.494

Asia WGS AF: 0.689 AC: 2389 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.6
DANN	Benign	0.36
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs11227802; hg19: chr11-56068101;