rs17067123

Variant names:

• chr4-179127208-C-T
• rs17067123

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 0.141 in 152,084 control chromosomes in the GnomAD database, including 1,936 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 0.14 (1936 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.416
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.405 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: 0.141 AC: 21426 AN: 151966 Hom.: 1931 Cov.: 32

Gnomad AFR AF: 0.144

Gnomad AMI AF: 0.116

Gnomad AMR AF: 0.231

Gnomad ASJ AF: 0.0715

Gnomad EAS AF: 0.421

Gnomad SAS AF: 0.238

Gnomad FIN AF: 0.0970

Gnomad MID AF: 0.134

Gnomad NFE AF: 0.102

Gnomad OTH AF: 0.143

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

GnomAD4 genome AF: 0.141 AC: 21449 AN: 152084 Hom.: 1936 Cov.: 32 AF XY: 0.147 AC XY: 10932 AN XY: 74338

African (AFR) AF: 0.144 AC: 5954 AN: 41480

American (AMR) AF: 0.232 AC: 3538 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.0715 AC: 248 AN: 3470

East Asian (EAS) AF: 0.420 AC: 2165 AN: 5156

South Asian (SAS) AF: 0.237 AC: 1145 AN: 4824

European-Finnish (FIN) AF: 0.0970 AC: 1026 AN: 10574

Middle Eastern (MID) AF: 0.134 AC: 39 AN: 292

European-Non Finnish (NFE) AF: 0.102 AC: 6926 AN: 68006

Other (OTH) AF: 0.143 AC: 302 AN: 2112

Alfa AF: 0.123 Hom.: 6824

Bravo AF: 0.152

Asia WGS AF: 0.310 AC: 1076 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.7
DANN	Benign	0.58
PhyloP100		0.42

Splicing

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

Other links and lift over

dbSNP: rs17067123; hg19: chr4-180048362;