3-67093414-T-A

Variant names:

• chr3-67093414-T-A
• rs4392363

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 0.322 in 152,044 control chromosomes in the GnomAD database, including 8,593 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 0.32 (8593 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.932
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.459 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: 0.322 AC: 48852 AN: 151926 Hom.: 8580 Cov.: 32

Gnomad AFR AF: 0.464

Gnomad AMI AF: 0.230

Gnomad AMR AF: 0.280

Gnomad ASJ AF: 0.237

Gnomad EAS AF: 0.450

Gnomad SAS AF: 0.338

Gnomad FIN AF: 0.173

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.262

Gnomad OTH AF: 0.314

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

GnomAD4 genome AF: 0.322 AC: 48897 AN: 152044 Hom.: 8593 Cov.: 32 AF XY: 0.316 AC XY: 23515 AN XY: 74346

African (AFR) AF: 0.465 AC: 19259 AN: 41452

American (AMR) AF: 0.279 AC: 4256 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.237 AC: 823 AN: 3468

East Asian (EAS) AF: 0.449 AC: 2325 AN: 5176

South Asian (SAS) AF: 0.337 AC: 1626 AN: 4820

European-Finnish (FIN) AF: 0.173 AC: 1828 AN: 10590

Middle Eastern (MID) AF: 0.282 AC: 83 AN: 294

European-Non Finnish (NFE) AF: 0.262 AC: 17825 AN: 67968

Other (OTH) AF: 0.313 AC: 662 AN: 2114

Alfa AF: 0.290 Hom.: 949

Bravo AF: 0.337

Asia WGS AF: 0.370 AC: 1283 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.29
DANN	Benign	0.29
PhyloP100		-0.93

Splicing

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

Other links and lift over

dbSNP: rs4392363; hg19: chr3-67143838;