rs1932420

Variant names:

• chr9-24901569-T-C
• rs1932420

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.261 in 152,030 control chromosomes in the GnomAD database, including 5,864 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 0.26 (5864 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.145
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.28).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.432 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.261 AC: 39629 AN: 151912 Hom.: 5879 Cov.: 32

Gnomad AFR AF: 0.121

Gnomad AMI AF: 0.170

Gnomad AMR AF: 0.317

Gnomad ASJ AF: 0.414

Gnomad EAS AF: 0.447

Gnomad SAS AF: 0.324

Gnomad FIN AF: 0.273

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.303

Gnomad OTH AF: 0.311

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

GnomAD4 genome AF: 0.261 AC: 39622 AN: 152030 Hom.: 5864 Cov.: 32 AF XY: 0.262 AC XY: 19493 AN XY: 74316

African (AFR) AF: 0.122 AC: 5043 AN: 41490

American (AMR) AF: 0.317 AC: 4834 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.414 AC: 1436 AN: 3470

East Asian (EAS) AF: 0.447 AC: 2299 AN: 5144

South Asian (SAS) AF: 0.324 AC: 1563 AN: 4824

European-Finnish (FIN) AF: 0.273 AC: 2890 AN: 10576

Middle Eastern (MID) AF: 0.524 AC: 153 AN: 292

European-Non Finnish (NFE) AF: 0.303 AC: 20606 AN: 67968

Other (OTH) AF: 0.306 AC: 643 AN: 2102

Alfa AF: 0.291 Hom.: 3628

Bravo AF: 0.260

Asia WGS AF: 0.320 AC: 1114 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.28
CADD	Benign	16
DANN	Benign	0.64
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs1932420; hg19: chr9-24901567;