chr11-56408195-C-G

Variant names:

• chr11-56408195-C-G
• rs1945213

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 0.747 in 152,056 control chromosomes in the GnomAD database, including 42,453 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 0.75 (42453 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.43
• Publications: 19 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.789 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: 0.747 AC: 113444 AN: 151938 Hom.: 42414 Cov.: 32

Gnomad AFR AF: 0.765

Gnomad AMI AF: 0.737

Gnomad AMR AF: 0.800

Gnomad ASJ AF: 0.778

Gnomad EAS AF: 0.772

Gnomad SAS AF: 0.800

Gnomad FIN AF: 0.708

Gnomad MID AF: 0.696

Gnomad NFE AF: 0.722

Gnomad OTH AF: 0.773

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

GnomAD4 genome AF: 0.747 AC: 113537 AN: 152056 Hom.: 42453 Cov.: 32 AF XY: 0.747 AC XY: 55488 AN XY: 74314

African (AFR) AF: 0.764 AC: 31717 AN: 41490

American (AMR) AF: 0.801 AC: 12235 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.778 AC: 2696 AN: 3466

East Asian (EAS) AF: 0.772 AC: 3989 AN: 5168

South Asian (SAS) AF: 0.801 AC: 3862 AN: 4824

European-Finnish (FIN) AF: 0.708 AC: 7465 AN: 10550

Middle Eastern (MID) AF: 0.707 AC: 208 AN: 294

European-Non Finnish (NFE) AF: 0.722 AC: 49052 AN: 67958

Other (OTH) AF: 0.777 AC: 1641 AN: 2112

Alfa AF: 0.720 Hom.: 19141

Bravo AF: 0.759

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.018
DANN	Benign	0.28
PhyloP100		-3.4

Splicing

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

Other links and lift over

dbSNP: rs1945213; hg19: chr11-56175671;