rs13435101

Variant names:

• chr4-154528680-C-A
• rs13435101

Your query was ambiguous. Multiple possible variants found:

• chr4-154528680-C-A
• chr4-154528680-C-G
• chr4-154528680-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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;