4-135209793-C-T

Variant names:

• chr4-135209793-C-T
• rs13143611

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 0.501 in 151,274 control chromosomes in the GnomAD database, including 19,374 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 0.50 (19374 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.579
• Publications: 1 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 = 0.634 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: 0.501 AC: 75702 AN: 151154 Hom.: 19360 Cov.: 31

Gnomad AFR AF: 0.413

Gnomad AMI AF: 0.508

Gnomad AMR AF: 0.546

Gnomad ASJ AF: 0.505

Gnomad EAS AF: 0.653

Gnomad SAS AF: 0.391

Gnomad FIN AF: 0.586

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.527

Gnomad OTH AF: 0.504

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

GnomAD4 genome AF: 0.501 AC: 75764 AN: 151274 Hom.: 19374 Cov.: 31 AF XY: 0.504 AC XY: 37226 AN XY: 73850

African (AFR) AF: 0.413 AC: 17078 AN: 41328

American (AMR) AF: 0.546 AC: 8248 AN: 15110

Ashkenazi Jewish (ASJ) AF: 0.505 AC: 1744 AN: 3456

East Asian (EAS) AF: 0.653 AC: 3330 AN: 5102

South Asian (SAS) AF: 0.391 AC: 1879 AN: 4808

European-Finnish (FIN) AF: 0.586 AC: 6171 AN: 10536

Middle Eastern (MID) AF: 0.469 AC: 138 AN: 294

European-Non Finnish (NFE) AF: 0.527 AC: 35650 AN: 67636

Other (OTH) AF: 0.508 AC: 1064 AN: 2094

Alfa AF: 0.519 Hom.: 2672

Bravo AF: 0.499

Asia WGS AF: 0.514 AC: 1786 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.0
DANN	Benign	0.50
PhyloP100		0.58

Splicing

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

Other links and lift over

dbSNP: rs13143611; hg19: chr4-136130948;