rs9315439

Variant names:

• chr13-20271441-C-T
• rs9315439

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.268 AC: 11102 AN: 41466

American (AMR) AF: 0.304 AC: 4648 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.179 AC: 622 AN: 3468

East Asian (EAS) AF: 0.00791 AC: 41 AN: 5182

South Asian (SAS) AF: 0.132 AC: 634 AN: 4816

European-Finnish (FIN) AF: 0.199 AC: 2104 AN: 10564

Middle Eastern (MID) AF: 0.269 AC: 79 AN: 294

European-Non Finnish (NFE) AF: 0.248 AC: 16832 AN: 67970

Other (OTH) AF: 0.256 AC: 539 AN: 2108

Alfa AF: 0.252 Hom.: 8069

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
PhyloP100		-0.34

Splicing

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

Other links and lift over

dbSNP: rs9315439; hg19: chr13-20845580;