rs9315439

Positions:

• chr13-20271441-C-T

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 0.242 in 152,046 control chromosomes in the GnomAD database, including 4,617 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 0.24 (4617 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.338

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.297 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.242 AC: 36799 AN: 151928 Hom.: 4615 Cov.: 31

Gnomad AFR AF: 0.268

Gnomad AMI AF: 0.234

Gnomad AMR AF: 0.305

Gnomad ASJ AF: 0.179

Gnomad EAS AF: 0.00809

Gnomad SAS AF: 0.132

Gnomad FIN AF: 0.199

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.248

Gnomad OTH AF: 0.257

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

GnomAD4 genome AF: 0.242 AC: 36814 AN: 152046 Hom.: 4617 Cov.: 31 AF XY: 0.237 AC XY: 17579 AN XY: 74304

Gnomad4 AFR AF: 0.268

Gnomad4 AMR AF: 0.304

Gnomad4 ASJ AF: 0.179

Gnomad4 EAS AF: 0.00791

Gnomad4 SAS AF: 0.132

Gnomad4 FIN AF: 0.199

Gnomad4 NFE AF: 0.248

Gnomad4 OTH AF: 0.256

Alfa AF: 0.249 Hom.: 6203

Bravo AF: 0.253

Asia WGS AF: 0.104 AC: 362 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.24
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9315439; hg19: chr13-20845580;