rs17675487

Positions:

• chr2-23299618-A-G
• chr2-23299618-A-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 0.362 in 152,158 control chromosomes in the GnomAD database, including 10,694 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 0.36 (10694 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.01

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.64).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.62 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.362 AC: 55013 AN: 152038 Hom.: 10693 Cov.: 33

Gnomad AFR AF: 0.227

Gnomad AMI AF: 0.452

Gnomad AMR AF: 0.436

Gnomad ASJ AF: 0.520

Gnomad EAS AF: 0.638

Gnomad SAS AF: 0.337

Gnomad FIN AF: 0.395

Gnomad MID AF: 0.433

Gnomad NFE AF: 0.391

Gnomad OTH AF: 0.421

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

GnomAD4 genome AF: 0.362 AC: 55006 AN: 152158 Hom.: 10694 Cov.: 33 AF XY: 0.365 AC XY: 27163 AN XY: 74388

Gnomad4 AFR AF: 0.227

Gnomad4 AMR AF: 0.436

Gnomad4 ASJ AF: 0.520

Gnomad4 EAS AF: 0.638

Gnomad4 SAS AF: 0.337

Gnomad4 FIN AF: 0.395

Gnomad4 NFE AF: 0.391

Gnomad4 OTH AF: 0.416

Alfa AF: 0.337 Hom.: 2027

Bravo AF: 0.365

Asia WGS AF: 0.417 AC: 1451 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	8.9
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17675487; hg19: chr2-23522489;