rs9548988

chr13-39931373-C-T

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 0.438 in 151,902 control chromosomes in the GnomAD database, including 14,981 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 0.44 (14981 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.91

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.513 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: 0.438 AC: 66451 AN: 151784 Hom.: 14959 Cov.: 32

Gnomad AFR AF: 0.407

Gnomad AMI AF: 0.426

Gnomad AMR AF: 0.386

Gnomad ASJ AF: 0.632

Gnomad EAS AF: 0.398

Gnomad SAS AF: 0.529

Gnomad FIN AF: 0.326

Gnomad MID AF: 0.639

Gnomad NFE AF: 0.470

Gnomad OTH AF: 0.488

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

GnomAD4 genome AF: 0.438 AC: 66497 AN: 151902 Hom.: 14981 Cov.: 32 AF XY: 0.433 AC XY: 32165 AN XY: 74218

Gnomad4 AFR AF: 0.407

Gnomad4 AMR AF: 0.385

Gnomad4 ASJ AF: 0.632

Gnomad4 EAS AF: 0.399

Gnomad4 SAS AF: 0.530

Gnomad4 FIN AF: 0.326

Gnomad4 NFE AF: 0.470

Gnomad4 OTH AF: 0.491

Alfa AF: 0.463 Hom.: 6248

Bravo AF: 0.438

Asia WGS AF: 0.497 AC: 1733 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	0.095
Dann	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9548988; hg19: chr13-40505510;