chr3-22724978-T-G

Variant names:

• chr3-22724978-T-G
• rs1402366

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 0.125 in 152,246 control chromosomes in the GnomAD database, including 1,305 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 0.13 (1305 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.38

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.14 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: 0.125 AC: 19056 AN: 152128 Hom.: 1307 Cov.: 32

Gnomad AFR AF: 0.144

Gnomad AMI AF: 0.133

Gnomad AMR AF: 0.105

Gnomad ASJ AF: 0.128

Gnomad EAS AF: 0.0264

Gnomad SAS AF: 0.0381

Gnomad FIN AF: 0.117

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.133

Gnomad OTH AF: 0.127

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

GnomAD4 genome AF: 0.125 AC: 19057 AN: 152246 Hom.: 1305 Cov.: 32 AF XY: 0.121 AC XY: 8986 AN XY: 74444

Gnomad4 AFR AF: 0.143

Gnomad4 AMR AF: 0.105

Gnomad4 ASJ AF: 0.128

Gnomad4 EAS AF: 0.0258

Gnomad4 SAS AF: 0.0381

Gnomad4 FIN AF: 0.117

Gnomad4 NFE AF: 0.133

Gnomad4 OTH AF: 0.125

Alfa AF: 0.129 Hom.: 2013

Bravo AF: 0.129

Asia WGS AF: 0.0440 AC: 153 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	3.2
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1402366; hg19: chr3-22766469;