rs17088254

chr4-67325476-C-Gchr4-67325476-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 0.0444 in 152,222 control chromosomes in the GnomAD database, including 201 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 0.044 (201 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.504

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 (NFE) allele frequency at 95% confidence interval = 0.0611 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: 0.0445 AC: 6762 AN: 152104 Hom.: 201 Cov.: 32

Gnomad AFR AF: 0.0151

Gnomad AMI AF: 0.0318

Gnomad AMR AF: 0.0315

Gnomad ASJ AF: 0.0818

Gnomad EAS AF: 0.0565

Gnomad SAS AF: 0.0619

Gnomad FIN AF: 0.0348

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0627

Gnomad OTH AF: 0.0464

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

GnomAD4 genome AF: 0.0444 AC: 6756 AN: 152222 Hom.: 201 Cov.: 32 AF XY: 0.0434 AC XY: 3232 AN XY: 74400

Gnomad4 AFR AF: 0.0150

Gnomad4 AMR AF: 0.0315

Gnomad4 ASJ AF: 0.0818

Gnomad4 EAS AF: 0.0560

Gnomad4 SAS AF: 0.0621

Gnomad4 FIN AF: 0.0348

Gnomad4 NFE AF: 0.0627

Gnomad4 OTH AF: 0.0459

Alfa AF: 0.0217 Hom.: 8

Bravo AF: 0.0434

Asia WGS AF: 0.0510 AC: 177 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	1.2
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: rs17088254; hg19: chr4-68191194;