rs17665021

Variant names:

• chr18-27642247-T-G
• rs17665021

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.0103 AC: 427 AN: 41536

American (AMR) AF: 0.0426 AC: 650 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.110 AC: 380 AN: 3468

East Asian (EAS) AF: 0.000194 AC: 1 AN: 5148

South Asian (SAS) AF: 0.00768 AC: 37 AN: 4818

European-Finnish (FIN) AF: 0.0342 AC: 363 AN: 10614

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.0566 AC: 3846 AN: 67908

Other (OTH) AF: 0.0591 AC: 125 AN: 2116

Alfa AF: 0.0533 Hom.: 193

Bravo AF: 0.0392

Asia WGS AF: 0.00462 AC: 16 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	7.1
DANN	Benign	0.88
PhyloP100		0.65

Splicing

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

Other links and lift over

dbSNP: rs17665021; hg19: chr18-25222211;