rs17263755

chr18-75109329-C-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 0.04 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/exons	MANE	UniProt

Ensembl

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