rs2081748

Variant names:

• chr12-114879735-G-C
• rs2081748

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 0.06 in 152,150 control chromosomes in the GnomAD database, including 332 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 0.060 (332 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.242
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0941 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: 0.0599 AC: 9104 AN: 152032 Hom.: 328 Cov.: 32

Gnomad AFR AF: 0.0961

Gnomad AMI AF: 0.0430

Gnomad AMR AF: 0.0275

Gnomad ASJ AF: 0.0306

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.00974

Gnomad FIN AF: 0.0659

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0544

Gnomad OTH AF: 0.0498

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

GnomAD4 genome AF: 0.0600 AC: 9130 AN: 152150 Hom.: 332 Cov.: 32 AF XY: 0.0578 AC XY: 4296 AN XY: 74372

African (AFR) AF: 0.0966 AC: 4008 AN: 41502

American (AMR) AF: 0.0273 AC: 417 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0306 AC: 106 AN: 3466

East Asian (EAS) AF: 0.000386 AC: 2 AN: 5182

South Asian (SAS) AF: 0.00954 AC: 46 AN: 4820

European-Finnish (FIN) AF: 0.0659 AC: 698 AN: 10584

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.0544 AC: 3699 AN: 68002

Other (OTH) AF: 0.0492 AC: 104 AN: 2112

Alfa AF: 0.0638 Hom.: 46

Bravo AF: 0.0594

Asia WGS AF: 0.0170 AC: 59 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.8
DANN	Benign	0.74
PhyloP100		0.24

Splicing

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

Other links and lift over

dbSNP: rs2081748; hg19: chr12-115317540;