rs17032647

chr2-106206308-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0149 in 152,250 control chromosomes in the GnomAD database, including 35 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 0.015 (35 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0140

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BS1: Variant frequency is greater than expected in population amr. gnomad4 allele frequency = 0.0149 (2266/152250) while in subpopulation AMR AF= 0.0483 (738/15294). AF 95% confidence interval is 0.0454. There are 35 homozygotes in gnomad4. There are 1089 alleles in male gnomad4 subpopulation. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 31 gene

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: 0.0148 AC: 2259 AN: 152132 Hom.: 31 Cov.: 30

Gnomad AFR AF: 0.00372

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.0479

Gnomad ASJ AF: 0.0118

Gnomad EAS AF: 0.00829

Gnomad SAS AF: 0.0162

Gnomad FIN AF: 0.00810

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.0160

Gnomad OTH AF: 0.0158

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

GnomAD4 genome AF: 0.0149 AC: 2266 AN: 152250 Hom.: 35 Cov.: 30 AF XY: 0.0146 AC XY: 1089 AN XY: 74440

Gnomad4 AFR AF: 0.00371

Gnomad4 AMR AF: 0.0483

Gnomad4 ASJ AF: 0.0118

Gnomad4 EAS AF: 0.00831

Gnomad4 SAS AF: 0.0162

Gnomad4 FIN AF: 0.00810

Gnomad4 NFE AF: 0.0160

Gnomad4 OTH AF: 0.0156

Alfa AF: 0.0178 Hom.: 54

Bravo AF: 0.0191

Asia WGS AF: 0.0140 AC: 49 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	0.85
Dann	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17032647; hg19: chr2-106822764;