chr4-189602787-C-G

Position:

• chr4-189602787-C-G

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 0.785 in 152,138 control chromosomes in the GnomAD database, including 47,032 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 0.79 (47032 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.64

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.825 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.189602787C>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.785 AC: 119360 AN: 152020 Hom.: 46996 Cov.: 32

Gnomad AFR AF: 0.819

Gnomad AMI AF: 0.702

Gnomad AMR AF: 0.792

Gnomad ASJ AF: 0.689

Gnomad EAS AF: 0.846

Gnomad SAS AF: 0.740

Gnomad FIN AF: 0.845

Gnomad MID AF: 0.615

Gnomad NFE AF: 0.761

Gnomad OTH AF: 0.736

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

GnomAD4 genome AF: 0.785 AC: 119448 AN: 152138 Hom.: 47032 Cov.: 32 AF XY: 0.789 AC XY: 58673 AN XY: 74348

Gnomad4 AFR AF: 0.819

Gnomad4 AMR AF: 0.792

Gnomad4 ASJ AF: 0.689

Gnomad4 EAS AF: 0.846

Gnomad4 SAS AF: 0.739

Gnomad4 FIN AF: 0.845

Gnomad4 NFE AF: 0.761

Gnomad4 OTH AF: 0.732

Alfa AF: 0.784 Hom.: 5828

Bravo AF: 0.785

Asia WGS AF: 0.803 AC: 2790 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.22
DANN	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3911167; hg19: chr4-190523941;