rs1933182

chr1-109457216-A-Cchr1-109457216-A-Gchr1-109457216-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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;