4-178564978-T-A

Position:

• chr4-178564978-T-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 0.166 in 151,980 control chromosomes in the GnomAD database, including 2,918 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 0.17 (2918 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.112

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.434 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.166 AC: 25200 AN: 151862 Hom.: 2905 Cov.: 31

Gnomad AFR AF: 0.219

Gnomad AMI AF: 0.153

Gnomad AMR AF: 0.318

Gnomad ASJ AF: 0.111

Gnomad EAS AF: 0.449

Gnomad SAS AF: 0.143

Gnomad FIN AF: 0.0789

Gnomad MID AF: 0.0955

Gnomad NFE AF: 0.0962

Gnomad OTH AF: 0.177

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

GnomAD4 genome AF: 0.166 AC: 25245 AN: 151980 Hom.: 2918 Cov.: 31 AF XY: 0.168 AC XY: 12512 AN XY: 74282

Gnomad4 AFR AF: 0.219

Gnomad4 AMR AF: 0.319

Gnomad4 ASJ AF: 0.111

Gnomad4 EAS AF: 0.449

Gnomad4 SAS AF: 0.144

Gnomad4 FIN AF: 0.0789

Gnomad4 NFE AF: 0.0962

Gnomad4 OTH AF: 0.176

Alfa AF: 0.0224 Hom.: 8

Bravo AF: 0.192

Asia WGS AF: 0.278 AC: 965 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.0
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs727353; hg19: chr4-179486132;