rs7684572

Variant names:

• chr4-24759366-G-C
• rs7684572

Your query was ambiguous. Multiple possible variants found:

• chr4-24759366-G-C
• chr4-24759366-G-T

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 0.264 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.264 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

Gnomad4 AFR AF: 0.251

Gnomad4 AMR AF: 0.217

Gnomad4 ASJ AF: 0.265

Gnomad4 EAS AF: 0.391

Gnomad4 SAS AF: 0.345

Gnomad4 FIN AF: 0.186

Gnomad4 NFE AF: 0.278

Gnomad4 OTH AF: 0.260

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7684572; hg19: chr4-24760988;