rs9313548

Variant names:

• chr5-171534296-C-T
• rs9313548

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 0.554 in 152,004 control chromosomes in the GnomAD database, including 23,898 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 0.55 (23898 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.577

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.65 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: 0.554 AC: 84141 AN: 151886 Hom.: 23854 Cov.: 32

Gnomad AFR AF: 0.656

Gnomad AMI AF: 0.623

Gnomad AMR AF: 0.603

Gnomad ASJ AF: 0.597

Gnomad EAS AF: 0.346

Gnomad SAS AF: 0.365

Gnomad FIN AF: 0.510

Gnomad MID AF: 0.649

Gnomad NFE AF: 0.512

Gnomad OTH AF: 0.590

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

GnomAD4 genome AF: 0.554 AC: 84244 AN: 152004 Hom.: 23898 Cov.: 32 AF XY: 0.548 AC XY: 40717 AN XY: 74296

Gnomad4 AFR AF: 0.656

Gnomad4 AMR AF: 0.604

Gnomad4 ASJ AF: 0.597

Gnomad4 EAS AF: 0.346

Gnomad4 SAS AF: 0.365

Gnomad4 FIN AF: 0.510

Gnomad4 NFE AF: 0.512

Gnomad4 OTH AF: 0.590

Alfa AF: 0.523 Hom.: 9997

Bravo AF: 0.568

Asia WGS AF: 0.389 AC: 1354 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.9
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9313548; hg19: chr5-170961300;