rs9520256

Variant names:

• chr13-106977707-C-T
• rs9520256

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 0.451 in 151,980 control chromosomes in the GnomAD database, including 16,394 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 0.45 (16394 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.287

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.51 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: 0.452 AC: 68589 AN: 151864 Hom.: 16386 Cov.: 32

Gnomad AFR AF: 0.334

Gnomad AMI AF: 0.581

Gnomad AMR AF: 0.434

Gnomad ASJ AF: 0.447

Gnomad EAS AF: 0.178

Gnomad SAS AF: 0.467

Gnomad FIN AF: 0.660

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.514

Gnomad OTH AF: 0.423

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

GnomAD4 genome AF: 0.451 AC: 68618 AN: 151980 Hom.: 16394 Cov.: 32 AF XY: 0.455 AC XY: 33814 AN XY: 74292

Gnomad4 AFR AF: 0.334

Gnomad4 AMR AF: 0.435

Gnomad4 ASJ AF: 0.447

Gnomad4 EAS AF: 0.178

Gnomad4 SAS AF: 0.467

Gnomad4 FIN AF: 0.660

Gnomad4 NFE AF: 0.514

Gnomad4 OTH AF: 0.424

Alfa AF: 0.491 Hom.: 35166

Bravo AF: 0.427

Asia WGS AF: 0.335 AC: 1169 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.1
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9520256; hg19: chr13-107630055;