4-178189362-A-G

Position:

• chr4-178189362-A-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 0.411 in 151,928 control chromosomes in the GnomAD database, including 13,297 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 0.41 (13297 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.266

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.563 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: 0.411 AC: 62441 AN: 151810 Hom.: 13290 Cov.: 31

Gnomad AFR AF: 0.318

Gnomad AMI AF: 0.557

Gnomad AMR AF: 0.519

Gnomad ASJ AF: 0.410

Gnomad EAS AF: 0.580

Gnomad SAS AF: 0.451

Gnomad FIN AF: 0.399

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.427

Gnomad OTH AF: 0.444

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

GnomAD4 genome AF: 0.411 AC: 62478 AN: 151928 Hom.: 13297 Cov.: 31 AF XY: 0.415 AC XY: 30795 AN XY: 74274

Gnomad4 AFR AF: 0.318

Gnomad4 AMR AF: 0.520

Gnomad4 ASJ AF: 0.410

Gnomad4 EAS AF: 0.580

Gnomad4 SAS AF: 0.450

Gnomad4 FIN AF: 0.399

Gnomad4 NFE AF: 0.427

Gnomad4 OTH AF: 0.448

Alfa AF: 0.434 Hom.: 2480

Bravo AF: 0.417

Asia WGS AF: 0.540 AC: 1878 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.4
DANN	Benign	0.27

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2378811; hg19: chr4-179110516;