chr4-178123550-A-G

Variant names:

• chr4-178123550-A-G
• rs10031053

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 0.338 in 151,596 control chromosomes in the GnomAD database, including 8,818 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 0.34 (8818 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.23
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.356 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.338 AC: 51268 AN: 151478 Hom.: 8807 Cov.: 31

Gnomad AFR AF: 0.344

Gnomad AMI AF: 0.285

Gnomad AMR AF: 0.276

Gnomad ASJ AF: 0.332

Gnomad EAS AF: 0.221

Gnomad SAS AF: 0.338

Gnomad FIN AF: 0.342

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.360

Gnomad OTH AF: 0.302

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

GnomAD4 genome AF: 0.338 AC: 51314 AN: 151596 Hom.: 8818 Cov.: 31 AF XY: 0.337 AC XY: 24937 AN XY: 74074

African (AFR) AF: 0.344 AC: 14252 AN: 41380

American (AMR) AF: 0.276 AC: 4191 AN: 15192

Ashkenazi Jewish (ASJ) AF: 0.332 AC: 1153 AN: 3470

East Asian (EAS) AF: 0.221 AC: 1139 AN: 5160

South Asian (SAS) AF: 0.339 AC: 1631 AN: 4812

European-Finnish (FIN) AF: 0.342 AC: 3601 AN: 10522

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.360 AC: 24379 AN: 67748

Other (OTH) AF: 0.299 AC: 630 AN: 2106

Alfa AF: 0.329 Hom.: 4100

Bravo AF: 0.334

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.2
DANN	Benign	0.85
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs10031053; hg19: chr4-179044704;