chr4-179187526-C-T

Variant names:

• chr4-179187526-C-T
• rs10520419

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 0.0692 in 151,958 control chromosomes in the GnomAD database, including 976 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 0.069 (976 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.29

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.388 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: 0.0691 AC: 10497 AN: 151844 Hom.: 969 Cov.: 33

Gnomad AFR AF: 0.0344

Gnomad AMI AF: 0.126

Gnomad AMR AF: 0.215

Gnomad ASJ AF: 0.0321

Gnomad EAS AF: 0.403

Gnomad SAS AF: 0.105

Gnomad FIN AF: 0.0535

Gnomad MID AF: 0.0192

Gnomad NFE AF: 0.0338

Gnomad OTH AF: 0.0596

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

GnomAD4 genome AF: 0.0692 AC: 10518 AN: 151958 Hom.: 976 Cov.: 33 AF XY: 0.0757 AC XY: 5623 AN XY: 74272

Gnomad4 AFR AF: 0.0344

Gnomad4 AMR AF: 0.216

Gnomad4 ASJ AF: 0.0321

Gnomad4 EAS AF: 0.402

Gnomad4 SAS AF: 0.105

Gnomad4 FIN AF: 0.0535

Gnomad4 NFE AF: 0.0338

Gnomad4 OTH AF: 0.0599

Alfa AF: 0.0650 Hom.: 165

Bravo AF: 0.0817

Asia WGS AF: 0.256 AC: 888 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.32
DANN	Benign	0.19

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10520419; hg19: chr4-180108680;