2-118112002-G-T

Variant names:

• chr2-118112002-G-T
• rs12623648

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 0.0455 in 152,110 control chromosomes in the GnomAD database, including 232 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 0.045 (232 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.848
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.143 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: 0.0455 AC: 6917 AN: 151992 Hom.: 232 Cov.: 32

Gnomad AFR AF: 0.0100

Gnomad AMI AF: 0.0724

Gnomad AMR AF: 0.0535

Gnomad ASJ AF: 0.0386

Gnomad EAS AF: 0.152

Gnomad SAS AF: 0.123

Gnomad FIN AF: 0.0779

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0468

Gnomad OTH AF: 0.0383

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

GnomAD4 genome AF: 0.0455 AC: 6920 AN: 152110 Hom.: 232 Cov.: 32 AF XY: 0.0490 AC XY: 3643 AN XY: 74360

African (AFR) AF: 0.0100 AC: 415 AN: 41514

American (AMR) AF: 0.0535 AC: 817 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.0386 AC: 134 AN: 3468

East Asian (EAS) AF: 0.152 AC: 783 AN: 5166

South Asian (SAS) AF: 0.124 AC: 596 AN: 4816

European-Finnish (FIN) AF: 0.0779 AC: 824 AN: 10576

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.0467 AC: 3175 AN: 67990

Other (OTH) AF: 0.0412 AC: 87 AN: 2110

Alfa AF: 0.0425 Hom.: 182

Bravo AF: 0.0405

Asia WGS AF: 0.132 AC: 459 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.4
DANN	Benign	0.76
PhyloP100		0.85

Splicing

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

Other links and lift over

dbSNP: rs12623648; hg19: chr2-118869578;