rs9293162

Variant names:

• chr5-25065361-C-T
• rs9293162

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0413 in 152,144 control chromosomes in the GnomAD database, including 151 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 0.041 (151 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.960

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BS1: Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0413 (6288/152144) while in subpopulation AFR AF= 0.05 (2078/41534). AF 95% confidence interval is 0.0482. There are 151 homozygotes in gnomad4. There are 2995 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 151 gene

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: 0.0414 AC: 6294 AN: 152026 Hom.: 153 Cov.: 33

Gnomad AFR AF: 0.0502

Gnomad AMI AF: 0.0800

Gnomad AMR AF: 0.0278

Gnomad ASJ AF: 0.103

Gnomad EAS AF: 0.0231

Gnomad SAS AF: 0.0156

Gnomad FIN AF: 0.0202

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.0415

Gnomad OTH AF: 0.0483

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

GnomAD4 genome AF: 0.0413 AC: 6288 AN: 152144 Hom.: 151 Cov.: 33 AF XY: 0.0403 AC XY: 2995 AN XY: 74370

Gnomad4 AFR AF: 0.0500

Gnomad4 AMR AF: 0.0277

Gnomad4 ASJ AF: 0.103

Gnomad4 EAS AF: 0.0232

Gnomad4 SAS AF: 0.0158

Gnomad4 FIN AF: 0.0202

Gnomad4 NFE AF: 0.0415

Gnomad4 OTH AF: 0.0469

Alfa AF: 0.0431 Hom.: 183

Bravo AF: 0.0434

Asia WGS AF: 0.0170 AC: 60 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.9
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9293162; hg19: chr5-25065470;