rs2081748

Variant names:

• chr12-114879735-G-C
• rs2081748

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.0966

Gnomad4 AMR AF: 0.0273

Gnomad4 ASJ AF: 0.0306

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.00954

Gnomad4 FIN AF: 0.0659

Gnomad4 NFE AF: 0.0544

Gnomad4 OTH AF: 0.0492

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2081748; hg19: chr12-115317540;