rs17067123

chr4-179127208-C-T

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 0.141 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.141 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

Gnomad4 AFR AF: 0.144

Gnomad4 AMR AF: 0.232

Gnomad4 ASJ AF: 0.0715

Gnomad4 EAS AF: 0.420

Gnomad4 SAS AF: 0.237

Gnomad4 FIN AF: 0.0970

Gnomad4 NFE AF: 0.102

Gnomad4 OTH AF: 0.143

Alfa AF: 0.121 Hom.: 3259

Bravo AF: 0.152

Asia WGS AF: 0.310 AC: 1076 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	3.7
Dann	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17067123; hg19: chr4-180048362;