rs17088254

Variant names:

• chr4-67325476-C-G
• rs17088254

Your query was ambiguous. Multiple possible variants found:

• chr4-67325476-C-G
• chr4-67325476-C-T

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 0.0444 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
• Publications: 3 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 (NFE) allele frequency at 95% confidence interval = 0.0611 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: 0.0445 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

African (AFR) AF: 0.0150 AC: 625 AN: 41552

American (AMR) AF: 0.0315 AC: 481 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0818 AC: 284 AN: 3470

East Asian (EAS) AF: 0.0560 AC: 290 AN: 5178

South Asian (SAS) AF: 0.0621 AC: 299 AN: 4812

European-Finnish (FIN) AF: 0.0348 AC: 369 AN: 10592

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.0627 AC: 4264 AN: 68014

Other (OTH) AF: 0.0459 AC: 97 AN: 2114

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
PhyloP100		-0.50

Splicing

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

Other links and lift over

dbSNP: rs17088254; hg19: chr4-68191194;