rs2093403

Variant names:

• chr9-114849633-T-C
• rs2093403

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.128 in 152,232 control chromosomes in the GnomAD database, including 1,311 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 0.13 (1311 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.86
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.185 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: 0.128 AC: 19510 AN: 152114 Hom.: 1313 Cov.: 32

Gnomad AFR AF: 0.120

Gnomad AMI AF: 0.208

Gnomad AMR AF: 0.170

Gnomad ASJ AF: 0.0809

Gnomad EAS AF: 0.166

Gnomad SAS AF: 0.195

Gnomad FIN AF: 0.0835

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.125

Gnomad OTH AF: 0.124

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

GnomAD4 genome AF: 0.128 AC: 19533 AN: 152232 Hom.: 1311 Cov.: 32 AF XY: 0.129 AC XY: 9601 AN XY: 74422

African (AFR) AF: 0.120 AC: 4978 AN: 41544

American (AMR) AF: 0.170 AC: 2606 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0809 AC: 281 AN: 3472

East Asian (EAS) AF: 0.166 AC: 857 AN: 5178

South Asian (SAS) AF: 0.195 AC: 940 AN: 4820

European-Finnish (FIN) AF: 0.0835 AC: 886 AN: 10614

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.125 AC: 8506 AN: 68002

Other (OTH) AF: 0.124 AC: 262 AN: 2108

Alfa AF: 0.127 Hom.: 883

Bravo AF: 0.131

Asia WGS AF: 0.181 AC: 629 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	13
DANN	Benign	0.55
PhyloP100		1.9

Splicing

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

Other links and lift over

dbSNP: rs2093403; hg19: chr9-117611913;