3-58326570-A-G

Variant names:

• chr3-58326570-A-G
• rs7622074

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 0.347 in 152,004 control chromosomes in the GnomAD database, including 10,081 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 0.35 (10081 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.18
• Publications: 11 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.79 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: 0.347 AC: 52656 AN: 151886 Hom.: 10083 Cov.: 31

Gnomad AFR AF: 0.265

Gnomad AMI AF: 0.488

Gnomad AMR AF: 0.373

Gnomad ASJ AF: 0.274

Gnomad EAS AF: 0.811

Gnomad SAS AF: 0.553

Gnomad FIN AF: 0.403

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.333

Gnomad OTH AF: 0.356

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

GnomAD4 genome AF: 0.347 AC: 52686 AN: 152004 Hom.: 10081 Cov.: 31 AF XY: 0.358 AC XY: 26580 AN XY: 74282

African (AFR) AF: 0.265 AC: 10985 AN: 41442

American (AMR) AF: 0.373 AC: 5683 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.274 AC: 951 AN: 3470

East Asian (EAS) AF: 0.810 AC: 4195 AN: 5176

South Asian (SAS) AF: 0.552 AC: 2657 AN: 4816

European-Finnish (FIN) AF: 0.403 AC: 4250 AN: 10554

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.333 AC: 22663 AN: 67976

Other (OTH) AF: 0.361 AC: 764 AN: 2114

Alfa AF: 0.336 Hom.: 13749

Bravo AF: 0.337

Asia WGS AF: 0.647 AC: 2247 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.63
DANN	Benign	0.17
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs7622074; hg19: chr3-58312297;