4-113788117-T-C

Variant names:

• chr4-113788117-T-C
• rs13134836

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 0.306 in 151,942 control chromosomes in the GnomAD database, including 7,514 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 0.31 (7514 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.266
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.496 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: 0.306 AC: 46455 AN: 151824 Hom.: 7515 Cov.: 31

Gnomad AFR AF: 0.238

Gnomad AMI AF: 0.233

Gnomad AMR AF: 0.320

Gnomad ASJ AF: 0.297

Gnomad EAS AF: 0.476

Gnomad SAS AF: 0.512

Gnomad FIN AF: 0.316

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.317

Gnomad OTH AF: 0.312

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

GnomAD4 genome AF: 0.306 AC: 46485 AN: 151942 Hom.: 7514 Cov.: 31 AF XY: 0.310 AC XY: 23035 AN XY: 74254

African (AFR) AF: 0.238 AC: 9874 AN: 41466

American (AMR) AF: 0.320 AC: 4881 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.297 AC: 1029 AN: 3462

East Asian (EAS) AF: 0.475 AC: 2441 AN: 5136

South Asian (SAS) AF: 0.512 AC: 2468 AN: 4816

European-Finnish (FIN) AF: 0.316 AC: 3337 AN: 10570

Middle Eastern (MID) AF: 0.282 AC: 83 AN: 294

European-Non Finnish (NFE) AF: 0.317 AC: 21507 AN: 67912

Other (OTH) AF: 0.309 AC: 654 AN: 2116

Alfa AF: 0.315 Hom.: 30145

Bravo AF: 0.299

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.1
DANN	Benign	0.51
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs13134836; hg19: chr4-114709273;