rs13435101

chr4-154528680-C-Achr4-154528680-C-Gchr4-154528680-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 0.524 in 151,836 control chromosomes in the GnomAD database, including 21,145 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 0.52 (21145 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0630

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.672 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: 0.524 AC: 79557 AN: 151718 Hom.: 21133 Cov.: 32

Gnomad AFR AF: 0.506

Gnomad AMI AF: 0.486

Gnomad AMR AF: 0.458

Gnomad ASJ AF: 0.510

Gnomad EAS AF: 0.691

Gnomad SAS AF: 0.603

Gnomad FIN AF: 0.516

Gnomad MID AF: 0.541

Gnomad NFE AF: 0.534

Gnomad OTH AF: 0.534

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

GnomAD4 genome AF: 0.524 AC: 79602 AN: 151836 Hom.: 21145 Cov.: 32 AF XY: 0.525 AC XY: 38949 AN XY: 74218

Gnomad4 AFR AF: 0.506

Gnomad4 AMR AF: 0.458

Gnomad4 ASJ AF: 0.510

Gnomad4 EAS AF: 0.691

Gnomad4 SAS AF: 0.603

Gnomad4 FIN AF: 0.516

Gnomad4 NFE AF: 0.534

Gnomad4 OTH AF: 0.530

Alfa AF: 0.533 Hom.: 23524

Bravo AF: 0.518

Asia WGS AF: 0.634 AC: 2201 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.96
Dann	Benign	0.14

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13435101; hg19: chr4-155449832;