13-44903055-C-G

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.0224

Gnomad4 AMR AF: 0.0901

Gnomad4 ASJ AF: 0.172

Gnomad4 EAS AF: 0.000772

Gnomad4 SAS AF: 0.0584

Gnomad4 FIN AF: 0.0819

Gnomad4 NFE AF: 0.129

Gnomad4 OTH AF: 0.121

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9534003; hg19: chr13-45477190;