chr2-17122021-T-G

Variant names:

• chr2-17122021-T-G
• rs10495658

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 0.159 in 152,018 control chromosomes in the GnomAD database, including 2,341 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 0.16 (2341 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00400
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.201 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: 0.159 AC: 24167 AN: 151900 Hom.: 2339 Cov.: 32

Gnomad AFR AF: 0.0809

Gnomad AMI AF: 0.0779

Gnomad AMR AF: 0.123

Gnomad ASJ AF: 0.250

Gnomad EAS AF: 0.0264

Gnomad SAS AF: 0.115

Gnomad FIN AF: 0.296

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.203

Gnomad OTH AF: 0.142

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

GnomAD4 genome AF: 0.159 AC: 24175 AN: 152018 Hom.: 2341 Cov.: 32 AF XY: 0.162 AC XY: 12011 AN XY: 74330

African (AFR) AF: 0.0810 AC: 3360 AN: 41472

American (AMR) AF: 0.123 AC: 1879 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.250 AC: 867 AN: 3468

East Asian (EAS) AF: 0.0267 AC: 138 AN: 5176

South Asian (SAS) AF: 0.115 AC: 552 AN: 4818

European-Finnish (FIN) AF: 0.296 AC: 3119 AN: 10546

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.203 AC: 13823 AN: 67958

Other (OTH) AF: 0.141 AC: 298 AN: 2110

Alfa AF: 0.183 Hom.: 5137

Bravo AF: 0.144

Asia WGS AF: 0.0640 AC: 223 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.0
DANN	Benign	0.80
PhyloP100		-0.0040

Splicing

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

Other links and lift over

dbSNP: rs10495658; hg19: chr2-17303288;