rs17330110

Variant names:

• chr2-35884868-C-G
• rs17330110

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 0.179 in 152,146 control chromosomes in the GnomAD database, including 3,077 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 0.18 (3077 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.312
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.249 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.179 AC: 27176 AN: 152028 Hom.: 3076 Cov.: 32

Gnomad AFR AF: 0.0544

Gnomad AMI AF: 0.375

Gnomad AMR AF: 0.174

Gnomad ASJ AF: 0.202

Gnomad EAS AF: 0.0294

Gnomad SAS AF: 0.125

Gnomad FIN AF: 0.270

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.252

Gnomad OTH AF: 0.192

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

GnomAD4 genome AF: 0.179 AC: 27171 AN: 152146 Hom.: 3077 Cov.: 32 AF XY: 0.177 AC XY: 13126 AN XY: 74358

African (AFR) AF: 0.0545 AC: 2263 AN: 41556

American (AMR) AF: 0.173 AC: 2646 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.202 AC: 702 AN: 3470

East Asian (EAS) AF: 0.0294 AC: 152 AN: 5164

South Asian (SAS) AF: 0.125 AC: 600 AN: 4818

European-Finnish (FIN) AF: 0.270 AC: 2851 AN: 10576

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.252 AC: 17163 AN: 67982

Other (OTH) AF: 0.190 AC: 402 AN: 2116

Alfa AF: 0.215 Hom.: 497

Bravo AF: 0.163

Asia WGS AF: 0.0680 AC: 234 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.5
DANN	Benign	0.71
PhyloP100		-0.31

Splicing

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

Other links and lift over

dbSNP: rs17330110; hg19: chr2-36109934;