rs13434451

Variant names:

• chr4-24785282-A-G
• rs13434451

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 0.148 in 152,220 control chromosomes in the GnomAD database, including 2,127 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 0.15 (2127 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0460

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 (AFR) allele frequency at 95% confidence interval = 0.241 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: 0.148 AC: 22465 AN: 152102 Hom.: 2120 Cov.: 33

Gnomad AFR AF: 0.245

Gnomad AMI AF: 0.0340

Gnomad AMR AF: 0.208

Gnomad ASJ AF: 0.160

Gnomad EAS AF: 0.126

Gnomad SAS AF: 0.207

Gnomad FIN AF: 0.0582

Gnomad MID AF: 0.151

Gnomad NFE AF: 0.0876

Gnomad OTH AF: 0.138

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

GnomAD4 genome AF: 0.148 AC: 22505 AN: 152220 Hom.: 2127 Cov.: 33 AF XY: 0.149 AC XY: 11062 AN XY: 74424

Gnomad4 AFR AF: 0.245

Gnomad4 AMR AF: 0.209

Gnomad4 ASJ AF: 0.160

Gnomad4 EAS AF: 0.126

Gnomad4 SAS AF: 0.208

Gnomad4 FIN AF: 0.0582

Gnomad4 NFE AF: 0.0876

Gnomad4 OTH AF: 0.137

Alfa AF: 0.101 Hom.: 1678

Bravo AF: 0.161

Asia WGS AF: 0.181 AC: 631 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	2.1
DANN	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13434451; hg19: chr4-24786904;