rs592720

chr12-52574076-A-Gchr12-52574076-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Moderate BP6_Moderate BA1

The variant allele was found at a frequency of 0.794 in 152,166 control chromosomes in the GnomAD database, including 48,886 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.79 (48886 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.679

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.31).
• BP6: Variant 12-52574076-A-G is Benign according to our data. Variant chr12-52574076-A-G is described in ClinVar as [Benign]. Clinvar id is 1225607.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.945 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: 0.794 AC: 120744 AN: 152048 Hom.: 48823 Cov.: 32

Gnomad AFR AF: 0.953

Gnomad AMI AF: 0.805

Gnomad AMR AF: 0.679

Gnomad ASJ AF: 0.678

Gnomad EAS AF: 0.708

Gnomad SAS AF: 0.787

Gnomad FIN AF: 0.747

Gnomad MID AF: 0.696

Gnomad NFE AF: 0.745

Gnomad OTH AF: 0.772

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

GnomAD4 genome AF: 0.794 AC: 120864 AN: 152166 Hom.: 48886 Cov.: 32 AF XY: 0.789 AC XY: 58679 AN XY: 74366

Gnomad4 AFR AF: 0.953

Gnomad4 AMR AF: 0.679

Gnomad4 ASJ AF: 0.678

Gnomad4 EAS AF: 0.708

Gnomad4 SAS AF: 0.787

Gnomad4 FIN AF: 0.747

Gnomad4 NFE AF: 0.745

Gnomad4 OTH AF: 0.772

Alfa AF: 0.774 Hom.: 6412

Bravo AF: 0.794

Asia WGS AF: 0.771 AC: 2679 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Nov 12, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.31
Cadd	Benign	16
Dann	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs592720; hg19: chr12-52967860;