rs13130318

Variant names:

• chr4-154617318-T-G
• rs13130318

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.179 AC: 7426 AN: 41490

American (AMR) AF: 0.210 AC: 3204 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.149 AC: 517 AN: 3472

East Asian (EAS) AF: 0.451 AC: 2333 AN: 5168

South Asian (SAS) AF: 0.296 AC: 1424 AN: 4818

European-Finnish (FIN) AF: 0.305 AC: 3223 AN: 10568

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.242 AC: 16468 AN: 67994

Other (OTH) AF: 0.199 AC: 420 AN: 2106

Alfa AF: 0.208 Hom.: 726

Bravo AF: 0.224

Asia WGS AF: 0.314 AC: 1090 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.39
DANN	Benign	0.46
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs13130318; hg19: chr4-155538470;