rs4149570

Variant names:

• chr12-6342424-A-C
• rs4149570

Your query was ambiguous. Multiple possible variants found:

• chr12-6342424-A-C
• chr12-6342424-A-G
• chr12-6342424-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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

Jun 19, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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;