chr4-45173674-C-T

Variant names:

• chr4-45173674-C-T
• rs13130484

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.374 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

Gnomad4 AFR AF: 0.241

Gnomad4 AMR AF: 0.404

Gnomad4 ASJ AF: 0.446

Gnomad4 EAS AF: 0.282

Gnomad4 SAS AF: 0.395

Gnomad4 FIN AF: 0.505

Gnomad4 NFE AF: 0.430

Gnomad4 OTH AF: 0.376

Alfa AF: 0.419 Hom.: 27939

Bravo AF: 0.360

Asia WGS AF: 0.303 AC: 1054 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.3
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13130484; hg19: chr4-45175691;