rs17665021

Variant names:

• chr18-27642247-T-G
• rs17665021

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 0.0388 in 152,080 control chromosomes in the GnomAD database, including 175 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 0.039 (175 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.651

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0551 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: 0.0388 AC: 5899 AN: 151962 Hom.: 175 Cov.: 33

Gnomad AFR AF: 0.0103

Gnomad AMI AF: 0.0482

Gnomad AMR AF: 0.0426

Gnomad ASJ AF: 0.110

Gnomad EAS AF: 0.000194

Gnomad SAS AF: 0.00767

Gnomad FIN AF: 0.0342

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0566

Gnomad OTH AF: 0.0597

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

GnomAD4 genome AF: 0.0388 AC: 5898 AN: 152080 Hom.: 175 Cov.: 33 AF XY: 0.0371 AC XY: 2761 AN XY: 74370

Gnomad4 AFR AF: 0.0103

Gnomad4 AMR AF: 0.0426

Gnomad4 ASJ AF: 0.110

Gnomad4 EAS AF: 0.000194

Gnomad4 SAS AF: 0.00768

Gnomad4 FIN AF: 0.0342

Gnomad4 NFE AF: 0.0566

Gnomad4 OTH AF: 0.0591

Alfa AF: 0.0537 Hom.: 170

Bravo AF: 0.0392

Asia WGS AF: 0.00462 AC: 16 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	7.1
DANN	Benign	0.88

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17665021; hg19: chr18-25222211;