rs9544105

Positions:

• chr13-75984017-T-C

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 0.209 in 152,204 control chromosomes in the GnomAD database, including 4,216 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 0.21 (4216 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.340

ACMG classification

Verdict is Benign. Variant got -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 = 0.281 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.209 AC: 31754 AN: 152086 Hom.: 4214 Cov.: 32

Gnomad AFR AF: 0.0754

Gnomad AMI AF: 0.330

Gnomad AMR AF: 0.145

Gnomad ASJ AF: 0.192

Gnomad EAS AF: 0.111

Gnomad SAS AF: 0.182

Gnomad FIN AF: 0.395

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.285

Gnomad OTH AF: 0.191

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

GnomAD4 genome AF: 0.209 AC: 31761 AN: 152204 Hom.: 4216 Cov.: 32 AF XY: 0.212 AC XY: 15769 AN XY: 74420

Gnomad4 AFR AF: 0.0753

Gnomad4 AMR AF: 0.145

Gnomad4 ASJ AF: 0.192

Gnomad4 EAS AF: 0.111

Gnomad4 SAS AF: 0.182

Gnomad4 FIN AF: 0.395

Gnomad4 NFE AF: 0.285

Gnomad4 OTH AF: 0.191

Alfa AF: 0.255 Hom.: 7120

Bravo AF: 0.183

Asia WGS AF: 0.156 AC: 544 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	2.1
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9544105; hg19: chr13-76558153;