chr4-188876005-C-T

Position:

• chr4-188876005-C-T

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 0.0199 in 152,240 control chromosomes in the GnomAD database, including 47 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 0.020 (47 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.47

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0544 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: 0.0199 AC: 3027 AN: 152120 Hom.: 47 Cov.: 32

Gnomad AFR AF: 0.00570

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0217

Gnomad ASJ AF: 0.0427

Gnomad EAS AF: 0.0582

Gnomad SAS AF: 0.0605

Gnomad FIN AF: 0.0176

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0215

Gnomad OTH AF: 0.0244

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

GnomAD4 genome AF: 0.0199 AC: 3027 AN: 152240 Hom.: 47 Cov.: 32 AF XY: 0.0214 AC XY: 1591 AN XY: 74450

Gnomad4 AFR AF: 0.00571

Gnomad4 AMR AF: 0.0217

Gnomad4 ASJ AF: 0.0427

Gnomad4 EAS AF: 0.0582

Gnomad4 SAS AF: 0.0601

Gnomad4 FIN AF: 0.0176

Gnomad4 NFE AF: 0.0216

Gnomad4 OTH AF: 0.0242

Alfa AF: 0.0193 Hom.: 4

Bravo AF: 0.0195

Asia WGS AF: 0.0490 AC: 169 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.053
DANN	Benign	0.18

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1448730; hg19: chr4-189797159;