chr2-169438993-C-T

Variant names:

• chr2-169438993-C-T
• rs10170021

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 0.378 in 152,014 control chromosomes in the GnomAD database, including 12,434 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 0.38 (12434 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.627
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.593 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: 0.378 AC: 57369 AN: 151896 Hom.: 12413 Cov.: 32

Gnomad AFR AF: 0.599

Gnomad AMI AF: 0.253

Gnomad AMR AF: 0.292

Gnomad ASJ AF: 0.285

Gnomad EAS AF: 0.461

Gnomad SAS AF: 0.445

Gnomad FIN AF: 0.271

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.276

Gnomad OTH AF: 0.346

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

GnomAD4 genome AF: 0.378 AC: 57448 AN: 152014 Hom.: 12434 Cov.: 32 AF XY: 0.378 AC XY: 28074 AN XY: 74308

African (AFR) AF: 0.599 AC: 24827 AN: 41446

American (AMR) AF: 0.292 AC: 4457 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.285 AC: 988 AN: 3466

East Asian (EAS) AF: 0.461 AC: 2381 AN: 5166

South Asian (SAS) AF: 0.445 AC: 2144 AN: 4820

European-Finnish (FIN) AF: 0.271 AC: 2867 AN: 10562

Middle Eastern (MID) AF: 0.269 AC: 79 AN: 294

European-Non Finnish (NFE) AF: 0.276 AC: 18744 AN: 67974

Other (OTH) AF: 0.346 AC: 731 AN: 2112

Alfa AF: 0.312 Hom.: 11381

Bravo AF: 0.388

Asia WGS AF: 0.484 AC: 1682 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.2
DANN	Benign	0.28
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs10170021; hg19: chr2-170295503;