rs13435192

Variant names:

• chr4-154529006-C-T
• rs13435192

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 0.524 in 151,874 control chromosomes in the GnomAD database, including 21,153 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 (21153 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0250
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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 = 0.673 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: 79551 AN: 151756 Hom.: 21141 Cov.: 31

Gnomad AFR AF: 0.505

Gnomad AMI AF: 0.485

Gnomad AMR AF: 0.458

Gnomad ASJ AF: 0.510

Gnomad EAS AF: 0.692

Gnomad SAS AF: 0.603

Gnomad FIN AF: 0.515

Gnomad MID AF: 0.541

Gnomad NFE AF: 0.534

Gnomad OTH AF: 0.535

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

GnomAD4 genome AF: 0.524 AC: 79596 AN: 151874 Hom.: 21153 Cov.: 31 AF XY: 0.525 AC XY: 38959 AN XY: 74218

African (AFR) AF: 0.506 AC: 20932 AN: 41398

American (AMR) AF: 0.457 AC: 6977 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.510 AC: 1768 AN: 3466

East Asian (EAS) AF: 0.691 AC: 3572 AN: 5166

South Asian (SAS) AF: 0.603 AC: 2899 AN: 4810

European-Finnish (FIN) AF: 0.515 AC: 5421 AN: 10518

Middle Eastern (MID) AF: 0.534 AC: 157 AN: 294

European-Non Finnish (NFE) AF: 0.534 AC: 36309 AN: 67934

Other (OTH) AF: 0.531 AC: 1119 AN: 2108

Alfa AF: 0.518 Hom.: 7140

Bravo AF: 0.518

Asia WGS AF: 0.635 AC: 2205 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.4
DANN	Benign	0.64
PhyloP100		-0.025

Splicing

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

Other links and lift over

dbSNP: rs13435192; hg19: chr4-155450158;