rs13130318

chr4-154617318-T-G

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 0.232 in 152,090 control chromosomes in the GnomAD database, including 4,423 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 0.23 (4423 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.05

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.436 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.232 AC: 35262 AN: 151972 Hom.: 4421 Cov.: 32

Gnomad AFR AF: 0.179

Gnomad AMI AF: 0.252

Gnomad AMR AF: 0.210

Gnomad ASJ AF: 0.149

Gnomad EAS AF: 0.452

Gnomad SAS AF: 0.295

Gnomad FIN AF: 0.305

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.242

Gnomad OTH AF: 0.201

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

GnomAD4 genome AF: 0.232 AC: 35287 AN: 152090 Hom.: 4423 Cov.: 32 AF XY: 0.236 AC XY: 17537 AN XY: 74334

Gnomad4 AFR AF: 0.179

Gnomad4 AMR AF: 0.210

Gnomad4 ASJ AF: 0.149

Gnomad4 EAS AF: 0.451

Gnomad4 SAS AF: 0.296

Gnomad4 FIN AF: 0.305

Gnomad4 NFE AF: 0.242

Gnomad4 OTH AF: 0.199

Alfa AF: 0.227 Hom.: 512

Bravo AF: 0.224

Asia WGS AF: 0.314 AC: 1090 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.39
Dann	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13130318; hg19: chr4-155538470;