rs9293162

chr5-25065361-C-T

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. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 153 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;