4-178564978-T-A

Variant names:

• chr4-178564978-T-A
• rs727353

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.219 AC: 9088 AN: 41432

American (AMR) AF: 0.319 AC: 4863 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.111 AC: 384 AN: 3470

East Asian (EAS) AF: 0.449 AC: 2303 AN: 5130

South Asian (SAS) AF: 0.144 AC: 692 AN: 4820

European-Finnish (FIN) AF: 0.0789 AC: 835 AN: 10580

Middle Eastern (MID) AF: 0.103 AC: 30 AN: 292

European-Non Finnish (NFE) AF: 0.0962 AC: 6541 AN: 67988

Other (OTH) AF: 0.176 AC: 370 AN: 2106

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
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs727353; hg19: chr4-179486132;