rs2181829

chr9-2245401-G-Achr9-2245401-G-Cchr9-2245401-G-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 0.875 in 152,184 control chromosomes in the GnomAD database, including 58,485 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 0.88 (58485 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0370

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.945 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: 0.875 AC: 133037 AN: 152066 Hom.: 58421 Cov.: 31

Gnomad AFR AF: 0.953

Gnomad AMI AF: 0.860

Gnomad AMR AF: 0.879

Gnomad ASJ AF: 0.773

Gnomad EAS AF: 0.954

Gnomad SAS AF: 0.903

Gnomad FIN AF: 0.823

Gnomad MID AF: 0.820

Gnomad NFE AF: 0.833

Gnomad OTH AF: 0.854

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

GnomAD4 genome AF: 0.875 AC: 133161 AN: 152184 Hom.: 58485 Cov.: 31 AF XY: 0.876 AC XY: 65168 AN XY: 74382

Gnomad4 AFR AF: 0.953

Gnomad4 AMR AF: 0.879

Gnomad4 ASJ AF: 0.773

Gnomad4 EAS AF: 0.954

Gnomad4 SAS AF: 0.903

Gnomad4 FIN AF: 0.823

Gnomad4 NFE AF: 0.833

Gnomad4 OTH AF: 0.851

Alfa AF: 0.836 Hom.: 107171

Bravo AF: 0.884

Asia WGS AF: 0.902 AC: 3132 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.3
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: rs2181829; hg19: chr9-2245401;