rs9292715

Variant names:

• chr5-38681565-T-C
• rs9292715

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 0.0578 in 152,304 control chromosomes in the GnomAD database, including 643 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 0.058 (643 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.29

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.6).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.168 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: 0.0575 AC: 8754 AN: 152186 Hom.: 633 Cov.: 33

Gnomad AFR AF: 0.171

Gnomad AMI AF: 0.0230

Gnomad AMR AF: 0.0570

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.0173

Gnomad SAS AF: 0.0128

Gnomad FIN AF: 0.00988

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.00611

Gnomad OTH AF: 0.0435

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

GnomAD4 genome AF: 0.0578 AC: 8797 AN: 152304 Hom.: 643 Cov.: 33 AF XY: 0.0558 AC XY: 4156 AN XY: 74474

Gnomad4 AFR AF: 0.172

Gnomad4 AMR AF: 0.0568

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.0173

Gnomad4 SAS AF: 0.0126

Gnomad4 FIN AF: 0.00988

Gnomad4 NFE AF: 0.00610

Gnomad4 OTH AF: 0.0468

Alfa AF: 0.0377 Hom.: 60

Bravo AF: 0.0671

Asia WGS AF: 0.0550 AC: 189 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.60
CADD	Benign	14
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9292715; hg19: chr5-38681667;