7-21384925-C-T

Variant names:

• chr7-21384925-C-T
• rs4722020

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 0.808 in 152,028 control chromosomes in the GnomAD database, including 49,697 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 0.81 (49697 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.864

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.821 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: 0.808 AC: 122763 AN: 151910 Hom.: 49661 Cov.: 29

Gnomad AFR AF: 0.801

Gnomad AMI AF: 0.919

Gnomad AMR AF: 0.821

Gnomad ASJ AF: 0.789

Gnomad EAS AF: 0.841

Gnomad SAS AF: 0.716

Gnomad FIN AF: 0.839

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.810

Gnomad OTH AF: 0.790

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

GnomAD4 genome AF: 0.808 AC: 122856 AN: 152028 Hom.: 49697 Cov.: 29 AF XY: 0.807 AC XY: 59975 AN XY: 74334

Gnomad4 AFR AF: 0.801

Gnomad4 AMR AF: 0.821

Gnomad4 ASJ AF: 0.789

Gnomad4 EAS AF: 0.842

Gnomad4 SAS AF: 0.716

Gnomad4 FIN AF: 0.839

Gnomad4 NFE AF: 0.810

Gnomad4 OTH AF: 0.785

Alfa AF: 0.800 Hom.: 64448

Bravo AF: 0.806

Asia WGS AF: 0.759 AC: 2642 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	2.5
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4722020; hg19: chr7-21424543;