rs13355548

Variant names:

• chr5-31089242-G-A
• rs13355548

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 0.124 in 152,168 control chromosomes in the GnomAD database, including 1,332 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 0.12 (1332 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0260

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.156 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: 0.124 AC: 18903 AN: 152050 Hom.: 1333 Cov.: 32

Gnomad AFR AF: 0.159

Gnomad AMI AF: 0.205

Gnomad AMR AF: 0.0709

Gnomad ASJ AF: 0.0867

Gnomad EAS AF: 0.0166

Gnomad SAS AF: 0.0851

Gnomad FIN AF: 0.198

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.116

Gnomad OTH AF: 0.112

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

GnomAD4 genome AF: 0.124 AC: 18914 AN: 152168 Hom.: 1332 Cov.: 32 AF XY: 0.126 AC XY: 9403 AN XY: 74382

Gnomad4 AFR AF: 0.159

Gnomad4 AMR AF: 0.0707

Gnomad4 ASJ AF: 0.0867

Gnomad4 EAS AF: 0.0166

Gnomad4 SAS AF: 0.0852

Gnomad4 FIN AF: 0.198

Gnomad4 NFE AF: 0.116

Gnomad4 OTH AF: 0.111

Alfa AF: 0.117 Hom.: 429

Bravo AF: 0.115

Asia WGS AF: 0.0800 AC: 279 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	7.2
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: rs13355548; hg19: chr5-31089349;