rs2660845

chr12-96044775-G-Achr12-96044775-G-C

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 0.686 in 152,134 control chromosomes in the GnomAD database, including 36,303 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 0.69 (36303 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.79

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.726 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.686 AC: 104288 AN: 152016 Hom.: 36283 Cov.: 33

Gnomad AFR AF: 0.666

Gnomad AMI AF: 0.704

Gnomad AMR AF: 0.549

Gnomad ASJ AF: 0.680

Gnomad EAS AF: 0.438

Gnomad SAS AF: 0.673

Gnomad FIN AF: 0.802

Gnomad MID AF: 0.693

Gnomad NFE AF: 0.731

Gnomad OTH AF: 0.660

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

GnomAD4 genome AF: 0.686 AC: 104351 AN: 152134 Hom.: 36303 Cov.: 33 AF XY: 0.684 AC XY: 50855 AN XY: 74370

Gnomad4 AFR AF: 0.666

Gnomad4 AMR AF: 0.548

Gnomad4 ASJ AF: 0.680

Gnomad4 EAS AF: 0.439

Gnomad4 SAS AF: 0.672

Gnomad4 FIN AF: 0.802

Gnomad4 NFE AF: 0.731

Gnomad4 OTH AF: 0.662

Alfa AF: 0.710 Hom.: 55024

Bravo AF: 0.663

Asia WGS AF: 0.571 AC: 1986 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.062
Dann	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2660845; hg19: chr12-96438553;