1-221806025-C-T

Variant names:

• chr1-221806025-C-T
• rs11118864

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 0.0707 in 152,020 control chromosomes in the GnomAD database, including 533 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 0.071 (533 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0480

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 (AMR) allele frequency at 95% confidence interval = 0.101 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: 0.0708 AC: 10749 AN: 151902 Hom.: 533 Cov.: 32

Gnomad AFR AF: 0.0176

Gnomad AMI AF: 0.0855

Gnomad AMR AF: 0.105

Gnomad ASJ AF: 0.0343

Gnomad EAS AF: 0.0804

Gnomad SAS AF: 0.0469

Gnomad FIN AF: 0.144

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0866

Gnomad OTH AF: 0.0715

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

GnomAD4 genome AF: 0.0707 AC: 10747 AN: 152020 Hom.: 533 Cov.: 32 AF XY: 0.0744 AC XY: 5526 AN XY: 74284

Gnomad4 AFR AF: 0.0176

Gnomad4 AMR AF: 0.105

Gnomad4 ASJ AF: 0.0343

Gnomad4 EAS AF: 0.0800

Gnomad4 SAS AF: 0.0477

Gnomad4 FIN AF: 0.144

Gnomad4 NFE AF: 0.0866

Gnomad4 OTH AF: 0.0708

Alfa AF: 0.0732 Hom.: 84

Bravo AF: 0.0660

Asia WGS AF: 0.0670 AC: 233 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.1
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11118864; hg19: chr1-221979367;