4-45173674-C-T

Variant names:

• chr4-45173674-C-T
• rs13130484

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 0.374 in 151,942 control chromosomes in the GnomAD database, including 11,272 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 0.37 (11272 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0550
• Publications: 70 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 (NFE) allele frequency at 95% confidence interval = 0.425 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: 0.374 AC: 56747 AN: 151824 Hom.: 11271 Cov.: 32

Gnomad AFR AF: 0.241

Gnomad AMI AF: 0.320

Gnomad AMR AF: 0.404

Gnomad ASJ AF: 0.446

Gnomad EAS AF: 0.283

Gnomad SAS AF: 0.395

Gnomad FIN AF: 0.505

Gnomad MID AF: 0.396

Gnomad NFE AF: 0.430

Gnomad OTH AF: 0.380

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

GnomAD4 genome AF: 0.374 AC: 56757 AN: 151942 Hom.: 11272 Cov.: 32 AF XY: 0.376 AC XY: 27903 AN XY: 74234

African (AFR) AF: 0.241 AC: 9969 AN: 41426

American (AMR) AF: 0.404 AC: 6169 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.446 AC: 1546 AN: 3470

East Asian (EAS) AF: 0.282 AC: 1453 AN: 5148

South Asian (SAS) AF: 0.395 AC: 1908 AN: 4826

European-Finnish (FIN) AF: 0.505 AC: 5325 AN: 10548

Middle Eastern (MID) AF: 0.391 AC: 115 AN: 294

European-Non Finnish (NFE) AF: 0.430 AC: 29187 AN: 67938

Other (OTH) AF: 0.376 AC: 794 AN: 2112

Alfa AF: 0.409 Hom.: 57248

Bravo AF: 0.360

Asia WGS AF: 0.303 AC: 1054 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	4.3
DANN	Benign	0.79
PhyloP100		-0.055

Splicing

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

Other links and lift over

dbSNP: rs13130484; hg19: chr4-45175691;