rs17263755

Variant names:

• chr18-75109329-C-T
• rs17263755

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 0.04 in 152,208 control chromosomes in the GnomAD database, including 170 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 0.040 (170 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.19

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0725 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: 0.0400 AC: 6082 AN: 152090 Hom.: 169 Cov.: 33

Gnomad AFR AF: 0.00963

Gnomad AMI AF: 0.0297

Gnomad AMR AF: 0.0760

Gnomad ASJ AF: 0.0254

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0159

Gnomad FIN AF: 0.0386

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.0562

Gnomad OTH AF: 0.0455

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

GnomAD4 genome AF: 0.0400 AC: 6084 AN: 152208 Hom.: 170 Cov.: 33 AF XY: 0.0399 AC XY: 2967 AN XY: 74406

Gnomad4 AFR AF: 0.00961

Gnomad4 AMR AF: 0.0761

Gnomad4 ASJ AF: 0.0254

Gnomad4 EAS AF: 0.000194

Gnomad4 SAS AF: 0.0160

Gnomad4 FIN AF: 0.0386

Gnomad4 NFE AF: 0.0562

Gnomad4 OTH AF: 0.0450

Alfa AF: 0.0532 Hom.: 223

Bravo AF: 0.0423

Asia WGS AF: 0.0100 AC: 36 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.010
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17263755; hg19: chr18-72821285;