rs9506903

Variant names:

• chr13-22678007-T-C
• rs9506903

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 0.278 in 152,164 control chromosomes in the GnomAD database, including 6,734 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 0.28 (6734 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0720
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.361 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: 0.278 AC: 42208 AN: 152046 Hom.: 6721 Cov.: 33

Gnomad AFR AF: 0.135

Gnomad AMI AF: 0.494

Gnomad AMR AF: 0.350

Gnomad ASJ AF: 0.331

Gnomad EAS AF: 0.0656

Gnomad SAS AF: 0.278

Gnomad FIN AF: 0.233

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.365

Gnomad OTH AF: 0.279

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

GnomAD4 genome AF: 0.278 AC: 42239 AN: 152164 Hom.: 6734 Cov.: 33 AF XY: 0.271 AC XY: 20201 AN XY: 74416

African (AFR) AF: 0.135 AC: 5620 AN: 41504

American (AMR) AF: 0.350 AC: 5356 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.331 AC: 1149 AN: 3470

East Asian (EAS) AF: 0.0661 AC: 343 AN: 5188

South Asian (SAS) AF: 0.279 AC: 1346 AN: 4828

European-Finnish (FIN) AF: 0.233 AC: 2465 AN: 10584

Middle Eastern (MID) AF: 0.310 AC: 91 AN: 294

European-Non Finnish (NFE) AF: 0.365 AC: 24834 AN: 67990

Other (OTH) AF: 0.277 AC: 586 AN: 2114

Alfa AF: 0.338 Hom.: 6909

Bravo AF: 0.281

Asia WGS AF: 0.157 AC: 545 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.4
DANN	Benign	0.87
PhyloP100		-0.072

Splicing

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

Other links and lift over

dbSNP: rs9506903; hg19: chr13-23252146;