4-188064339-T-C

Position:

• chr4-188064339-T-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 0.65 in 151,434 control chromosomes in the GnomAD database, including 32,424 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 0.65 (32424 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.377

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.873 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.188064339T>C		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.650 AC: 98419 AN: 151316 Hom.: 32395 Cov.: 32

Gnomad AFR AF: 0.569

Gnomad AMI AF: 0.670

Gnomad AMR AF: 0.667

Gnomad ASJ AF: 0.778

Gnomad EAS AF: 0.894

Gnomad SAS AF: 0.535

Gnomad FIN AF: 0.621

Gnomad MID AF: 0.680

Gnomad NFE AF: 0.683

Gnomad OTH AF: 0.680

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

GnomAD4 genome AF: 0.650 AC: 98500 AN: 151434 Hom.: 32424 Cov.: 32 AF XY: 0.648 AC XY: 47925 AN XY: 73956

Gnomad4 AFR AF: 0.569

Gnomad4 AMR AF: 0.667

Gnomad4 ASJ AF: 0.778

Gnomad4 EAS AF: 0.894

Gnomad4 SAS AF: 0.535

Gnomad4 FIN AF: 0.621

Gnomad4 NFE AF: 0.683

Gnomad4 OTH AF: 0.683

Alfa AF: 0.678 Hom.: 50993

Bravo AF: 0.654

Asia WGS AF: 0.717 AC: 2489 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.8
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11132507; hg19: chr4-188985493;