rs17354568

Variant names:

• chr4-141470217-G-T
• rs17354568

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 0.207 in 152,068 control chromosomes in the GnomAD database, including 3,438 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 0.21 (3438 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0400

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.257 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: 0.207 AC: 31495 AN: 151946 Hom.: 3427 Cov.: 32

Gnomad AFR AF: 0.257

Gnomad AMI AF: 0.0932

Gnomad AMR AF: 0.264

Gnomad ASJ AF: 0.184

Gnomad EAS AF: 0.220

Gnomad SAS AF: 0.185

Gnomad FIN AF: 0.127

Gnomad MID AF: 0.217

Gnomad NFE AF: 0.180

Gnomad OTH AF: 0.201

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

GnomAD4 genome AF: 0.207 AC: 31547 AN: 152068 Hom.: 3438 Cov.: 32 AF XY: 0.207 AC XY: 15394 AN XY: 74350

Gnomad4 AFR AF: 0.257

Gnomad4 AMR AF: 0.264

Gnomad4 ASJ AF: 0.184

Gnomad4 EAS AF: 0.220

Gnomad4 SAS AF: 0.186

Gnomad4 FIN AF: 0.127

Gnomad4 NFE AF: 0.180

Gnomad4 OTH AF: 0.202

Alfa AF: 0.203 Hom.: 1145

Bravo AF: 0.219

Asia WGS AF: 0.212 AC: 740 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.0
DANN	Benign	0.22

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17354568; hg19: chr4-142391371;