12-107120863-A-G

Position:

• chr12-107120863-A-G

Variant summary

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

The ENST00000547679.1(ENSG00000257548):​n.128-1110A>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 0.36 in 152,154 control chromosomes in the GnomAD database, including 10,162 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 0.36 (10162 hom., cov: 33)
• Consequence: ENST00000547679.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.501

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.439 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000547679.1	n.128-1110A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.360 AC: 54769 AN: 152036 Hom.: 10151 Cov.: 33

Gnomad AFR AF: 0.291

Gnomad AMI AF: 0.360

Gnomad AMR AF: 0.447

Gnomad ASJ AF: 0.386

Gnomad EAS AF: 0.442

Gnomad SAS AF: 0.389

Gnomad FIN AF: 0.353

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.374

Gnomad OTH AF: 0.367

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

GnomAD4 genome AF: 0.360 AC: 54809 AN: 152154 Hom.: 10162 Cov.: 33 AF XY: 0.362 AC XY: 26955 AN XY: 74380

Gnomad4 AFR AF: 0.291

Gnomad4 AMR AF: 0.448

Gnomad4 ASJ AF: 0.386

Gnomad4 EAS AF: 0.443

Gnomad4 SAS AF: 0.389

Gnomad4 FIN AF: 0.353

Gnomad4 NFE AF: 0.374

Gnomad4 OTH AF: 0.362

Alfa AF: 0.374 Hom.: 5828

Bravo AF: 0.366

Asia WGS AF: 0.356 AC: 1237 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.39
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: rs1921141; hg19: chr12-107514641;