4-133071026-A-C

Position:

• chr4-133071026-A-C

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 0.457 in 151,876 control chromosomes in the GnomAD database, including 15,965 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 0.46 (15965 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.42

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.482 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.133071026A>C		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.457 AC: 69413 AN: 151756 Hom.: 15955 Cov.: 32

Gnomad AFR AF: 0.488

Gnomad AMI AF: 0.601

Gnomad AMR AF: 0.482

Gnomad ASJ AF: 0.427

Gnomad EAS AF: 0.335

Gnomad SAS AF: 0.427

Gnomad FIN AF: 0.407

Gnomad MID AF: 0.529

Gnomad NFE AF: 0.452

Gnomad OTH AF: 0.442

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

GnomAD4 genome AF: 0.457 AC: 69455 AN: 151876 Hom.: 15965 Cov.: 32 AF XY: 0.454 AC XY: 33714 AN XY: 74212

Gnomad4 AFR AF: 0.488

Gnomad4 AMR AF: 0.482

Gnomad4 ASJ AF: 0.427

Gnomad4 EAS AF: 0.336

Gnomad4 SAS AF: 0.427

Gnomad4 FIN AF: 0.407

Gnomad4 NFE AF: 0.452

Gnomad4 OTH AF: 0.437

Alfa AF: 0.455 Hom.: 4298

Bravo AF: 0.467

Asia WGS AF: 0.368 AC: 1280 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.11
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs984369; hg19: chr4-133992181;