1-30399349-C-T

Variant names:

• chr1-30399349-C-T
• rs3907322

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 0.231 in 152,034 control chromosomes in the GnomAD database, including 4,931 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 (4931 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.614
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.389 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: 0.231 AC: 35115 AN: 151916 Hom.: 4919 Cov.: 31

Gnomad AFR AF: 0.394

Gnomad AMI AF: 0.0899

Gnomad AMR AF: 0.156

Gnomad ASJ AF: 0.161

Gnomad EAS AF: 0.269

Gnomad SAS AF: 0.335

Gnomad FIN AF: 0.174

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.154

Gnomad OTH AF: 0.208

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

GnomAD4 genome AF: 0.231 AC: 35164 AN: 152034 Hom.: 4931 Cov.: 31 AF XY: 0.233 AC XY: 17327 AN XY: 74300

African (AFR) AF: 0.394 AC: 16327 AN: 41430

American (AMR) AF: 0.156 AC: 2389 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.161 AC: 557 AN: 3470

East Asian (EAS) AF: 0.269 AC: 1382 AN: 5134

South Asian (SAS) AF: 0.335 AC: 1609 AN: 4808

European-Finnish (FIN) AF: 0.174 AC: 1839 AN: 10584

Middle Eastern (MID) AF: 0.201 AC: 59 AN: 294

European-Non Finnish (NFE) AF: 0.154 AC: 10469 AN: 67992

Other (OTH) AF: 0.213 AC: 451 AN: 2116

Alfa AF: 0.154 Hom.: 713

Bravo AF: 0.236

Asia WGS AF: 0.305 AC: 1058 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.054
DANN	Benign	0.69
PhyloP100		-0.61

Splicing

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

Other links and lift over

dbSNP: rs3907322; hg19: chr1-30872196;