rs10993160

Variant names:

• chr9-94306644-A-G
• rs10993160

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 0.0449 in 152,266 control chromosomes in the GnomAD database, including 397 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 0.045 (397 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.216

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 = 0.195 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: 0.0450 AC: 6849 AN: 152148 Hom.: 399 Cov.: 32

Gnomad AFR AF: 0.0110

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.151

Gnomad ASJ AF: 0.0340

Gnomad EAS AF: 0.206

Gnomad SAS AF: 0.0599

Gnomad FIN AF: 0.0331

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0314

Gnomad OTH AF: 0.0559

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

GnomAD4 genome AF: 0.0449 AC: 6839 AN: 152266 Hom.: 397 Cov.: 32 AF XY: 0.0489 AC XY: 3640 AN XY: 74464

Gnomad4 AFR AF: 0.0110

Gnomad4 AMR AF: 0.151

Gnomad4 ASJ AF: 0.0340

Gnomad4 EAS AF: 0.206

Gnomad4 SAS AF: 0.0602

Gnomad4 FIN AF: 0.0331

Gnomad4 NFE AF: 0.0314

Gnomad4 OTH AF: 0.0539

Alfa AF: 0.0368 Hom.: 176

Bravo AF: 0.0554

Asia WGS AF: 0.120 AC: 417 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	1.2
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10993160; hg19: chr9-97068926;