chr4-4856163-T-A

Variant names:

• chr4-4856163-T-A
• rs13104352

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 0.533 in 151,654 control chromosomes in the GnomAD database, including 23,791 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 (23791 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.204

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.767 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: 0.533 AC: 80754 AN: 151536 Hom.: 23733 Cov.: 31

Gnomad AFR AF: 0.774

Gnomad AMI AF: 0.262

Gnomad AMR AF: 0.563

Gnomad ASJ AF: 0.450

Gnomad EAS AF: 0.654

Gnomad SAS AF: 0.635

Gnomad FIN AF: 0.463

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.383

Gnomad OTH AF: 0.517

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

GnomAD4 genome AF: 0.533 AC: 80873 AN: 151654 Hom.: 23791 Cov.: 31 AF XY: 0.541 AC XY: 40051 AN XY: 74076

Gnomad4 AFR AF: 0.774

Gnomad4 AMR AF: 0.564

Gnomad4 ASJ AF: 0.450

Gnomad4 EAS AF: 0.655

Gnomad4 SAS AF: 0.635

Gnomad4 FIN AF: 0.463

Gnomad4 NFE AF: 0.383

Gnomad4 OTH AF: 0.517

Alfa AF: 0.261 Hom.: 482

Bravo AF: 0.547

Asia WGS AF: 0.679 AC: 2364 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	0.76
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13104352; hg19: chr4-4857890;