rs9548988

Variant names:

• chr13-39931373-C-T
• rs9548988

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;