4-24759366-G-C

Variant names:

• chr4-24759366-G-C
• rs7684572

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 0.264 in 152,052 control chromosomes in the GnomAD database, including 5,441 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 0.26 (5441 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.950
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.377 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: 0.264 AC: 40151 AN: 151934 Hom.: 5441 Cov.: 32

Gnomad AFR AF: 0.251

Gnomad AMI AF: 0.360

Gnomad AMR AF: 0.217

Gnomad ASJ AF: 0.265

Gnomad EAS AF: 0.390

Gnomad SAS AF: 0.343

Gnomad FIN AF: 0.186

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.278

Gnomad OTH AF: 0.261

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

GnomAD4 genome AF: 0.264 AC: 40159 AN: 152052 Hom.: 5441 Cov.: 32 AF XY: 0.259 AC XY: 19237 AN XY: 74316

African (AFR) AF: 0.251 AC: 10412 AN: 41464

American (AMR) AF: 0.217 AC: 3317 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.265 AC: 920 AN: 3470

East Asian (EAS) AF: 0.391 AC: 2018 AN: 5164

South Asian (SAS) AF: 0.345 AC: 1655 AN: 4798

European-Finnish (FIN) AF: 0.186 AC: 1971 AN: 10570

Middle Eastern (MID) AF: 0.299 AC: 88 AN: 294

European-Non Finnish (NFE) AF: 0.278 AC: 18901 AN: 67978

Other (OTH) AF: 0.260 AC: 549 AN: 2112

Alfa AF: 0.127 Hom.: 190

Bravo AF: 0.266

Asia WGS AF: 0.321 AC: 1116 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	12
DANN	Benign	0.55
PhyloP100		0.95

Splicing

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

Other links and lift over

dbSNP: rs7684572; hg19: chr4-24760988;