rs9548988

Variant names:

• chr13-39931373-C-T
• rs9548988

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 13 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.407 AC: 16835 AN: 41396

American (AMR) AF: 0.385 AC: 5882 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.632 AC: 2190 AN: 3466

East Asian (EAS) AF: 0.399 AC: 2057 AN: 5160

South Asian (SAS) AF: 0.530 AC: 2551 AN: 4814

European-Finnish (FIN) AF: 0.326 AC: 3435 AN: 10528

Middle Eastern (MID) AF: 0.646 AC: 190 AN: 294

European-Non Finnish (NFE) AF: 0.470 AC: 31936 AN: 67944

Other (OTH) AF: 0.491 AC: 1033 AN: 2106

Alfa AF: 0.460 Hom.: 8951

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
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs9548988; hg19: chr13-40505510;