chr2-88129315-G-T

Variant names:

• chr2-88129315-G-T
• rs2970901

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 0.402 in 151,992 control chromosomes in the GnomAD database, including 13,297 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 0.40 (13297 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.265
• Publications: 13 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.458 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.403 AC: 61160 AN: 151874 Hom.: 13295 Cov.: 32

Gnomad AFR AF: 0.270

Gnomad AMI AF: 0.492

Gnomad AMR AF: 0.448

Gnomad ASJ AF: 0.416

Gnomad EAS AF: 0.205

Gnomad SAS AF: 0.221

Gnomad FIN AF: 0.639

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.463

Gnomad OTH AF: 0.411

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

GnomAD4 genome AF: 0.402 AC: 61174 AN: 151992 Hom.: 13297 Cov.: 32 AF XY: 0.404 AC XY: 30037 AN XY: 74304

African (AFR) AF: 0.269 AC: 11163 AN: 41458

American (AMR) AF: 0.448 AC: 6857 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.416 AC: 1443 AN: 3472

East Asian (EAS) AF: 0.205 AC: 1059 AN: 5164

South Asian (SAS) AF: 0.222 AC: 1071 AN: 4820

European-Finnish (FIN) AF: 0.639 AC: 6744 AN: 10548

Middle Eastern (MID) AF: 0.388 AC: 114 AN: 294

European-Non Finnish (NFE) AF: 0.463 AC: 31413 AN: 67920

Other (OTH) AF: 0.408 AC: 861 AN: 2112

Alfa AF: 0.428 Hom.: 7893

Bravo AF: 0.385

Asia WGS AF: 0.224 AC: 781 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.70
DANN	Benign	0.47
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs2970901; hg19: chr2-88428834;