rs9421801

Variant names:

• chr10-47316507-T-C
• rs9421801

Your query was ambiguous. Multiple possible variants found:

• chr10-47316507-T-C
• chr10-47316507-T-G

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 0.921 in 152,138 control chromosomes in the GnomAD database, including 64,637 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 0.92 (64637 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0630

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.936 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: 0.921 AC: 139978 AN: 152020 Hom.: 64586 Cov.: 30

Gnomad AFR AF: 0.916

Gnomad AMI AF: 0.996

Gnomad AMR AF: 0.903

Gnomad ASJ AF: 0.909

Gnomad EAS AF: 0.743

Gnomad SAS AF: 0.813

Gnomad FIN AF: 0.963

Gnomad MID AF: 0.914

Gnomad NFE AF: 0.942

Gnomad OTH AF: 0.922

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

GnomAD4 genome AF: 0.921 AC: 140091 AN: 152138 Hom.: 64637 Cov.: 30 AF XY: 0.919 AC XY: 68318 AN XY: 74350

Gnomad4 AFR AF: 0.916

Gnomad4 AMR AF: 0.903

Gnomad4 ASJ AF: 0.909

Gnomad4 EAS AF: 0.743

Gnomad4 SAS AF: 0.814

Gnomad4 FIN AF: 0.963

Gnomad4 NFE AF: 0.942

Gnomad4 OTH AF: 0.922

Alfa AF: 0.932 Hom.: 45879

Bravo AF: 0.917

Asia WGS AF: 0.788 AC: 2742 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	7.6
DANN	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9421801; hg19: chr10-48422855;