rs1933182

Variant names:

• chr1-109457216-A-C
• rs1933182

Your query was ambiguous. Multiple possible variants found:

• chr1-109457216-A-C
• chr1-109457216-A-G
• chr1-109457216-A-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 0.635 in 151,922 control chromosomes in the GnomAD database, including 32,475 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 0.64 (32475 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.304

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.937 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: 0.636 AC: 96489 AN: 151804 Hom.: 32456 Cov.: 30

Gnomad AFR AF: 0.407

Gnomad AMI AF: 0.689

Gnomad AMR AF: 0.771

Gnomad ASJ AF: 0.805

Gnomad EAS AF: 0.959

Gnomad SAS AF: 0.729

Gnomad FIN AF: 0.667

Gnomad MID AF: 0.706

Gnomad NFE AF: 0.697

Gnomad OTH AF: 0.687

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

GnomAD4 genome AF: 0.635 AC: 96527 AN: 151922 Hom.: 32475 Cov.: 30 AF XY: 0.639 AC XY: 47418 AN XY: 74242

Gnomad4 AFR AF: 0.406

Gnomad4 AMR AF: 0.772

Gnomad4 ASJ AF: 0.805

Gnomad4 EAS AF: 0.959

Gnomad4 SAS AF: 0.730

Gnomad4 FIN AF: 0.667

Gnomad4 NFE AF: 0.697

Gnomad4 OTH AF: 0.691

Alfa AF: 0.712 Hom.: 43856

Bravo AF: 0.639

Asia WGS AF: 0.795 AC: 2762 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.3
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1933182; hg19: chr1-109999838;