rs17183114

chr4-181301574-G-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 0.125 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;