rs56211063

Variant names:

• chr9-114823617-G-C
• rs56211063

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 0.0464 in 152,170 control chromosomes in the GnomAD database, including 546 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 0.046 (546 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.908

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.263 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: 0.0462 AC: 7027 AN: 152052 Hom.: 536 Cov.: 32

Gnomad AFR AF: 0.0446

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.128

Gnomad ASJ AF: 0.0141

Gnomad EAS AF: 0.274

Gnomad SAS AF: 0.0502

Gnomad FIN AF: 0.0960

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.00603

Gnomad OTH AF: 0.0435

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

GnomAD4 genome AF: 0.0464 AC: 7063 AN: 152170 Hom.: 546 Cov.: 32 AF XY: 0.0541 AC XY: 4024 AN XY: 74394

Gnomad4 AFR AF: 0.0453

Gnomad4 AMR AF: 0.128

Gnomad4 ASJ AF: 0.0141

Gnomad4 EAS AF: 0.274

Gnomad4 SAS AF: 0.0494

Gnomad4 FIN AF: 0.0960

Gnomad4 NFE AF: 0.00603

Gnomad4 OTH AF: 0.0459

Alfa AF: 0.0285 Hom.: 24

Bravo AF: 0.0535

Asia WGS AF: 0.144 AC: 501 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	6.2
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs56211063; hg19: chr9-117585897;