5-35239048-C-T

Variant names:

• chr5-35239048-C-T
• rs9292582

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 0.317 in 151,520 control chromosomes in the GnomAD database, including 8,683 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 0.32 (8683 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.16

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.442 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: 0.317 AC: 48056 AN: 151402 Hom.: 8679 Cov.: 31

Gnomad AFR AF: 0.161

Gnomad AMI AF: 0.377

Gnomad AMR AF: 0.293

Gnomad ASJ AF: 0.389

Gnomad EAS AF: 0.0907

Gnomad SAS AF: 0.458

Gnomad FIN AF: 0.375

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.410

Gnomad OTH AF: 0.341

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

GnomAD4 genome AF: 0.317 AC: 48060 AN: 151520 Hom.: 8683 Cov.: 31 AF XY: 0.318 AC XY: 23559 AN XY: 74004

Gnomad4 AFR AF: 0.161

Gnomad4 AMR AF: 0.292

Gnomad4 ASJ AF: 0.389

Gnomad4 EAS AF: 0.0907

Gnomad4 SAS AF: 0.458

Gnomad4 FIN AF: 0.375

Gnomad4 NFE AF: 0.410

Gnomad4 OTH AF: 0.345

Alfa AF: 0.342 Hom.: 1173

Bravo AF: 0.297

Asia WGS AF: 0.295 AC: 1025 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.57
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9292582; hg19: chr5-35239150;