rs13434451

Positions:

• chr4-24785282-A-G

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;