4-13008468-C-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.329 in 152,010 control chromosomes in the GnomAD database, including 8,482 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 0.33 (8482 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.26

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.24).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.4 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: 0.329 AC: 49987 AN: 151892 Hom.: 8475 Cov.: 32

Gnomad AFR AF: 0.281

Gnomad AMI AF: 0.384

Gnomad AMR AF: 0.276

Gnomad ASJ AF: 0.235

Gnomad EAS AF: 0.287

Gnomad SAS AF: 0.413

Gnomad FIN AF: 0.346

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.370

Gnomad OTH AF: 0.304

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

GnomAD4 genome AF: 0.329 AC: 50006 AN: 152010 Hom.: 8482 Cov.: 32 AF XY: 0.328 AC XY: 24329 AN XY: 74274

Gnomad4 AFR AF: 0.281

Gnomad4 AMR AF: 0.275

Gnomad4 ASJ AF: 0.235

Gnomad4 EAS AF: 0.287

Gnomad4 SAS AF: 0.415

Gnomad4 FIN AF: 0.346

Gnomad4 NFE AF: 0.370

Gnomad4 OTH AF: 0.303

Alfa AF: 0.339 Hom.: 1627

Bravo AF: 0.317

Asia WGS AF: 0.365 AC: 1269 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.24
Cadd	Benign	19
Dann	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2056117; hg19: chr4-13010092;