4-11094134-G-A

Position:

• chr4-11094134-G-A

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 0.507 in 151,920 control chromosomes in the GnomAD database, including 23,055 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 0.51 (23055 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0900

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.803 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.507 AC: 76911 AN: 151802 Hom.: 22995 Cov.: 33

Gnomad AFR AF: 0.810

Gnomad AMI AF: 0.387

Gnomad AMR AF: 0.489

Gnomad ASJ AF: 0.373

Gnomad EAS AF: 0.797

Gnomad SAS AF: 0.470

Gnomad FIN AF: 0.461

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.324

Gnomad OTH AF: 0.483

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

GnomAD4 genome AF: 0.507 AC: 77027 AN: 151920 Hom.: 23055 Cov.: 33 AF XY: 0.515 AC XY: 38253 AN XY: 74238

Gnomad4 AFR AF: 0.810

Gnomad4 AMR AF: 0.490

Gnomad4 ASJ AF: 0.373

Gnomad4 EAS AF: 0.798

Gnomad4 SAS AF: 0.468

Gnomad4 FIN AF: 0.461

Gnomad4 NFE AF: 0.323

Gnomad4 OTH AF: 0.486

Alfa AF: 0.435 Hom.: 2068

Bravo AF: 0.525

Asia WGS AF: 0.626 AC: 2156 AN: 3446

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.87
DANN	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4697843; hg19: chr4-11095758;