4-99325780-C-T

Variant names:

• chr4-99325780-C-T
• rs9307239

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 0.457 in 151,822 control chromosomes in the GnomAD database, including 16,816 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 0.46 (16816 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06
• Publications: 11 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.792 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: 0.457 AC: 69385 AN: 151704 Hom.: 16807 Cov.: 31

Gnomad AFR AF: 0.550

Gnomad AMI AF: 0.512

Gnomad AMR AF: 0.372

Gnomad ASJ AF: 0.343

Gnomad EAS AF: 0.812

Gnomad SAS AF: 0.656

Gnomad FIN AF: 0.407

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.393

Gnomad OTH AF: 0.439

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

GnomAD4 genome AF: 0.457 AC: 69429 AN: 151822 Hom.: 16816 Cov.: 31 AF XY: 0.463 AC XY: 34385 AN XY: 74220

African (AFR) AF: 0.549 AC: 22744 AN: 41394

American (AMR) AF: 0.372 AC: 5665 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.343 AC: 1190 AN: 3470

East Asian (EAS) AF: 0.812 AC: 4189 AN: 5158

South Asian (SAS) AF: 0.654 AC: 3144 AN: 4806

European-Finnish (FIN) AF: 0.407 AC: 4287 AN: 10538

Middle Eastern (MID) AF: 0.364 AC: 107 AN: 294

European-Non Finnish (NFE) AF: 0.393 AC: 26712 AN: 67900

Other (OTH) AF: 0.439 AC: 927 AN: 2110

Alfa AF: 0.408 Hom.: 21267

Bravo AF: 0.454

Asia WGS AF: 0.635 AC: 2208 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.6
DANN	Benign	0.79
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs9307239; hg19: chr4-100246937;