rs1945213

Variant names:

• chr11-56408195-C-G
• rs1945213

Your query was ambiguous. Multiple possible variants found:

• chr11-56408195-C-G
• chr11-56408195-C-T

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.764

Gnomad4 AMR AF: 0.801

Gnomad4 ASJ AF: 0.778

Gnomad4 EAS AF: 0.772

Gnomad4 SAS AF: 0.801

Gnomad4 FIN AF: 0.708

Gnomad4 NFE AF: 0.722

Gnomad4 OTH AF: 0.777

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1945213; hg19: chr11-56175671;