7-21384925-C-T

Variant names:

• chr7-21384925-C-T
• rs4722020

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 0.808 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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.801 AC: 33208 AN: 41476

American (AMR) AF: 0.821 AC: 12542 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.789 AC: 2740 AN: 3472

East Asian (EAS) AF: 0.842 AC: 4337 AN: 5152

South Asian (SAS) AF: 0.716 AC: 3444 AN: 4808

European-Finnish (FIN) AF: 0.839 AC: 8864 AN: 10562

Middle Eastern (MID) AF: 0.616 AC: 180 AN: 292

European-Non Finnish (NFE) AF: 0.810 AC: 55044 AN: 67964

Other (OTH) AF: 0.785 AC: 1659 AN: 2114

Alfa AF: 0.801 Hom.: 89936

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
PhyloP100		-0.86

Splicing

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

Other links and lift over

dbSNP: rs4722020; hg19: chr7-21424543;