12-121046146-T-G

Variant names:

• chr12-121046146-T-G
• rs2708104

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 0.619 in 151,984 control chromosomes in the GnomAD database, including 29,191 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 0.62 (29191 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.943
• Publications: 14 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.726 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: 0.619 AC: 93997 AN: 151866 Hom.: 29186 Cov.: 31

Gnomad AFR AF: 0.634

Gnomad AMI AF: 0.463

Gnomad AMR AF: 0.562

Gnomad ASJ AF: 0.624

Gnomad EAS AF: 0.614

Gnomad SAS AF: 0.747

Gnomad FIN AF: 0.580

Gnomad MID AF: 0.691

Gnomad NFE AF: 0.621

Gnomad OTH AF: 0.636

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

GnomAD4 genome AF: 0.619 AC: 94026 AN: 151984 Hom.: 29191 Cov.: 31 AF XY: 0.618 AC XY: 45925 AN XY: 74274

African (AFR) AF: 0.633 AC: 26225 AN: 41438

American (AMR) AF: 0.562 AC: 8569 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.624 AC: 2166 AN: 3470

East Asian (EAS) AF: 0.614 AC: 3171 AN: 5168

South Asian (SAS) AF: 0.746 AC: 3596 AN: 4820

European-Finnish (FIN) AF: 0.580 AC: 6121 AN: 10550

Middle Eastern (MID) AF: 0.688 AC: 201 AN: 292

European-Non Finnish (NFE) AF: 0.621 AC: 42208 AN: 67968

Other (OTH) AF: 0.639 AC: 1348 AN: 2110

Alfa AF: 0.618 Hom.: 118014

Bravo AF: 0.611

Asia WGS AF: 0.660 AC: 2294 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.8
DANN	Benign	0.25
PhyloP100		-0.94

Splicing

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

Other links and lift over

dbSNP: rs2708104; hg19: chr12-121483949;