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. The variant received -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
• Publications: 146 publications found

ACMG classification

Our verdict: Benign. The variant received -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 VariationId 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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.886 AC: 36779 AN: 41500

American (AMR) AF: 0.717 AC: 10947 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.673 AC: 2331 AN: 3464

East Asian (EAS) AF: 0.484 AC: 2504 AN: 5174

South Asian (SAS) AF: 0.668 AC: 3212 AN: 4808

European-Finnish (FIN) AF: 0.648 AC: 6830 AN: 10540

Middle Eastern (MID) AF: 0.626 AC: 184 AN: 294

European-Non Finnish (NFE) AF: 0.603 AC: 40956 AN: 67960

Other (OTH) AF: 0.687 AC: 1451 AN: 2112

Alfa AF: 0.630 Hom.: 86755

Bravo AF: 0.703

Asia WGS AF: 0.622 AC: 2165 AN: 3478

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.8
DANN	Benign	0.72
PhyloP100		-0.52
PromoterAI		-0.011	Neutral

Splicing

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

Other links and lift over

dbSNP: rs4149570; hg19: chr12-6451590;