rs17183114

Variant names:

• chr4-181301574-G-T
• rs17183114

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 0.125 in 152,004 control chromosomes in the GnomAD database, including 1,306 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 0.13 (1306 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.67

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.158 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: 0.125 AC: 19015 AN: 151886 Hom.: 1307 Cov.: 32

Gnomad AFR AF: 0.0958

Gnomad AMI AF: 0.0504

Gnomad AMR AF: 0.102

Gnomad ASJ AF: 0.106

Gnomad EAS AF: 0.0390

Gnomad SAS AF: 0.0455

Gnomad FIN AF: 0.138

Gnomad MID AF: 0.105

Gnomad NFE AF: 0.160

Gnomad OTH AF: 0.132

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

GnomAD4 genome AF: 0.125 AC: 19018 AN: 152004 Hom.: 1306 Cov.: 32 AF XY: 0.122 AC XY: 9026 AN XY: 74286

Gnomad4 AFR AF: 0.0956

Gnomad4 AMR AF: 0.102

Gnomad4 ASJ AF: 0.106

Gnomad4 EAS AF: 0.0391

Gnomad4 SAS AF: 0.0455

Gnomad4 FIN AF: 0.138

Gnomad4 NFE AF: 0.160

Gnomad4 OTH AF: 0.131

Alfa AF: 0.150 Hom.: 2841

Bravo AF: 0.123

Asia WGS AF: 0.0460 AC: 160 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.10
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17183114; hg19: chr4-182222727;