chr3-30701070-C-T

Variant names:

• chr3-30701070-C-T
• rs304822

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 0.233 in 152,056 control chromosomes in the GnomAD database, including 4,548 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 0.23 (4548 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.107
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.358 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.233 AC: 35439 AN: 151938 Hom.: 4551 Cov.: 32

Gnomad AFR AF: 0.130

Gnomad AMI AF: 0.288

Gnomad AMR AF: 0.323

Gnomad ASJ AF: 0.296

Gnomad EAS AF: 0.371

Gnomad SAS AF: 0.332

Gnomad FIN AF: 0.188

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.261

Gnomad OTH AF: 0.245

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

GnomAD4 genome AF: 0.233 AC: 35450 AN: 152056 Hom.: 4548 Cov.: 32 AF XY: 0.232 AC XY: 17220 AN XY: 74316

African (AFR) AF: 0.130 AC: 5394 AN: 41490

American (AMR) AF: 0.324 AC: 4940 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.296 AC: 1027 AN: 3468

East Asian (EAS) AF: 0.371 AC: 1912 AN: 5148

South Asian (SAS) AF: 0.331 AC: 1594 AN: 4822

European-Finnish (FIN) AF: 0.188 AC: 1991 AN: 10588

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.261 AC: 17738 AN: 67958

Other (OTH) AF: 0.247 AC: 522 AN: 2114

Alfa AF: 0.261 Hom.: 9169

Bravo AF: 0.238

Asia WGS AF: 0.377 AC: 1312 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.9
DANN	Benign	0.36
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs304822; hg19: chr3-30742562;