chr4-180155034-T-C

Variant names:

• chr4-180155034-T-C
• rs13129209

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 0.53 in 152,086 control chromosomes in the GnomAD database, including 25,056 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 0.53 (25056 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0410

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.692 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: 0.530 AC: 80589 AN: 151968 Hom.: 25058 Cov.: 33

Gnomad AFR AF: 0.187

Gnomad AMI AF: 0.481

Gnomad AMR AF: 0.550

Gnomad ASJ AF: 0.586

Gnomad EAS AF: 0.711

Gnomad SAS AF: 0.632

Gnomad FIN AF: 0.730

Gnomad MID AF: 0.586

Gnomad NFE AF: 0.680

Gnomad OTH AF: 0.546

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

GnomAD4 genome AF: 0.530 AC: 80598 AN: 152086 Hom.: 25056 Cov.: 33 AF XY: 0.537 AC XY: 39887 AN XY: 74334

Gnomad4 AFR AF: 0.187

Gnomad4 AMR AF: 0.549

Gnomad4 ASJ AF: 0.586

Gnomad4 EAS AF: 0.711

Gnomad4 SAS AF: 0.632

Gnomad4 FIN AF: 0.730

Gnomad4 NFE AF: 0.680

Gnomad4 OTH AF: 0.547

Alfa AF: 0.656 Hom.: 53535

Bravo AF: 0.503

Asia WGS AF: 0.600 AC: 2088 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	7.9
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13129209; hg19: chr4-181076187;