rs4149570

chr12-6342424-A-Cchr12-6342424-A-Gchr12-6342424-A-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The variant allele was found at a frequency of 0.695 in 152,036 control chromosomes in the GnomAD database, including 38,090 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.70 (38090 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.518

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BP6: Variant 12-6342424-A-C is Benign according to our data. Variant chr12-6342424-A-C is described in ClinVar as [Benign]. Clinvar id is 675609.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.879 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: 0.695 AC: 105608 AN: 151918 Hom.: 38033 Cov.: 31

Gnomad AFR AF: 0.886

Gnomad AMI AF: 0.584

Gnomad AMR AF: 0.717

Gnomad ASJ AF: 0.673

Gnomad EAS AF: 0.484

Gnomad SAS AF: 0.668

Gnomad FIN AF: 0.648

Gnomad MID AF: 0.649

Gnomad NFE AF: 0.603

Gnomad OTH AF: 0.686

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

GnomAD4 genome AF: 0.695 AC: 105725 AN: 152036 Hom.: 38090 Cov.: 31 AF XY: 0.698 AC XY: 51829 AN XY: 74296

Gnomad4 AFR AF: 0.886

Gnomad4 AMR AF: 0.717

Gnomad4 ASJ AF: 0.673

Gnomad4 EAS AF: 0.484

Gnomad4 SAS AF: 0.668

Gnomad4 FIN AF: 0.648

Gnomad4 NFE AF: 0.603

Gnomad4 OTH AF: 0.687

Alfa AF: 0.621 Hom.: 35358

Bravo AF: 0.703

Asia WGS AF: 0.622 AC: 2165 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

Jun 19, 2018

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	1.8
Dann	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4149570; hg19: chr12-6451590;