chr12-53865825-A-G

Position:

• chr12-53865825-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000663306.1(ENSG00000286069):​n.480-9330A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.889 in 152,150 control chromosomes in the GnomAD database, including 61,381 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 0.89 (61381 hom., cov: 31)
• Consequence: ENST00000663306.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0960

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.948 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107984525	XR_002957415.2	n.451+15413A>G		intron_variant, non_coding_transcript_variant
LOC107984525	XR_001749153.2	n.282-9330A>G		intron_variant, non_coding_transcript_variant
LOC107984525	XR_007063319.1	n.1401-9330A>G		intron_variant, non_coding_transcript_variant
LOC107984525	XR_007063320.1	n.229-9330A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000663306.1	n.480-9330A>G		intron_variant, non_coding_transcript_variant
	ENST00000652339.1	n.509+4947A>G		intron_variant, non_coding_transcript_variant
	ENST00000654713.1	n.317+15413A>G		intron_variant, non_coding_transcript_variant
	ENST00000656247.1	n.344+15413A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.889 AC: 135170 AN: 152032 Hom.: 61350 Cov.: 31

Gnomad AFR AF: 0.908

Gnomad AMI AF: 0.992

Gnomad AMR AF: 0.745

Gnomad ASJ AF: 0.950

Gnomad EAS AF: 0.339

Gnomad SAS AF: 0.836

Gnomad FIN AF: 0.865

Gnomad MID AF: 0.943

Gnomad NFE AF: 0.954

Gnomad OTH AF: 0.896

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

GnomAD4 genome AF: 0.889 AC: 135241 AN: 152150 Hom.: 61381 Cov.: 31 AF XY: 0.879 AC XY: 65362 AN XY: 74368

Gnomad4 AFR AF: 0.908

Gnomad4 AMR AF: 0.744

Gnomad4 ASJ AF: 0.950

Gnomad4 EAS AF: 0.339

Gnomad4 SAS AF: 0.836

Gnomad4 FIN AF: 0.865

Gnomad4 NFE AF: 0.954

Gnomad4 OTH AF: 0.891

Alfa AF: 0.908 Hom.: 14548

Bravo AF: 0.879

Asia WGS AF: 0.622 AC: 2166 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.6
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs796720; hg19: chr12-54259609;