chr13-44903055-C-G

Variant names:

• chr13-44903055-C-G
• rs9534003

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.087 in 152,200 control chromosomes in the GnomAD database, including 741 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 0.087 (741 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.948
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.35).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.127 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: 0.0871 AC: 13244 AN: 152082 Hom.: 740 Cov.: 32

Gnomad AFR AF: 0.0225

Gnomad AMI AF: 0.0954

Gnomad AMR AF: 0.0903

Gnomad ASJ AF: 0.172

Gnomad EAS AF: 0.000770

Gnomad SAS AF: 0.0577

Gnomad FIN AF: 0.0819

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.129

Gnomad OTH AF: 0.122

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

GnomAD4 genome AF: 0.0870 AC: 13240 AN: 152200 Hom.: 741 Cov.: 32 AF XY: 0.0849 AC XY: 6313 AN XY: 74382

African (AFR) AF: 0.0224 AC: 931 AN: 41550

American (AMR) AF: 0.0901 AC: 1378 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.172 AC: 597 AN: 3472

East Asian (EAS) AF: 0.000772 AC: 4 AN: 5182

South Asian (SAS) AF: 0.0584 AC: 281 AN: 4812

European-Finnish (FIN) AF: 0.0819 AC: 866 AN: 10580

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.129 AC: 8777 AN: 68002

Other (OTH) AF: 0.121 AC: 256 AN: 2110

Alfa AF: 0.0489 Hom.: 31

Bravo AF: 0.0861

Asia WGS AF: 0.0240 AC: 84 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.35
CADD	Benign	13
DANN	Benign	0.51
PhyloP100		0.95

Splicing

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

Other links and lift over

dbSNP: rs9534003; hg19: chr13-45477190;