4-24785282-A-G

Variant names:

• chr4-24785282-A-G
• rs13434451

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 0.148 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
• Publications: 5 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 (AFR) allele frequency at 95% confidence interval = 0.241 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	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

African (AFR) AF: 0.245 AC: 10165 AN: 41522

American (AMR) AF: 0.209 AC: 3190 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.160 AC: 555 AN: 3468

East Asian (EAS) AF: 0.126 AC: 655 AN: 5190

South Asian (SAS) AF: 0.208 AC: 1001 AN: 4824

European-Finnish (FIN) AF: 0.0582 AC: 617 AN: 10606

Middle Eastern (MID) AF: 0.155 AC: 45 AN: 290

European-Non Finnish (NFE) AF: 0.0876 AC: 5956 AN: 68008

Other (OTH) AF: 0.137 AC: 290 AN: 2114

Alfa AF: 0.107 Hom.: 4406

Bravo AF: 0.161

Asia WGS AF: 0.181 AC: 631 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.1
DANN	Benign	0.87
PhyloP100		0.046

Splicing

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

Other links and lift over

dbSNP: rs13434451; hg19: chr4-24786904;