rs4390476

Positions:

• chr13-84024435-A-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 0.0484 in 152,290 control chromosomes in the GnomAD database, including 271 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 0.048 (271 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.132

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0759 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: 0.0484 AC: 7371 AN: 152172 Hom.: 271 Cov.: 32

Gnomad AFR AF: 0.0133

Gnomad AMI AF: 0.0417

Gnomad AMR AF: 0.0410

Gnomad ASJ AF: 0.0499

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0153

Gnomad FIN AF: 0.0491

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0777

Gnomad OTH AF: 0.0458

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

GnomAD4 genome AF: 0.0484 AC: 7370 AN: 152290 Hom.: 271 Cov.: 32 AF XY: 0.0459 AC XY: 3421 AN XY: 74456

Gnomad4 AFR AF: 0.0132

Gnomad4 AMR AF: 0.0409

Gnomad4 ASJ AF: 0.0499

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.0153

Gnomad4 FIN AF: 0.0491

Gnomad4 NFE AF: 0.0777

Gnomad4 OTH AF: 0.0454

Alfa AF: 0.0639 Hom.: 101

Bravo AF: 0.0470

Asia WGS AF: 0.00837 AC: 30 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.6
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4390476; hg19: chr13-84598570;