rs9520256

Variant names:

• chr13-106977707-C-T
• rs9520256

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 0.451 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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.334 AC: 13835 AN: 41456

American (AMR) AF: 0.435 AC: 6637 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.447 AC: 1547 AN: 3462

East Asian (EAS) AF: 0.178 AC: 918 AN: 5164

South Asian (SAS) AF: 0.467 AC: 2250 AN: 4820

European-Finnish (FIN) AF: 0.660 AC: 6972 AN: 10564

Middle Eastern (MID) AF: 0.395 AC: 116 AN: 294

European-Non Finnish (NFE) AF: 0.514 AC: 34918 AN: 67924

Other (OTH) AF: 0.424 AC: 895 AN: 2112

Alfa AF: 0.487 Hom.: 71227

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
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs9520256; hg19: chr13-107630055;