12-107097814-A-G

Position:

• chr12-107097814-A-G

Variant summary

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

The ENST00000547679.1(ENSG00000257548):​n.127+344A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.504 in 151,882 control chromosomes in the GnomAD database, including 20,248 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 0.50 (20248 hom., cov: 30)
• Consequence: ENSG00000257548 ENST00000547679.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.209

Genes affected

ENSG00000257548 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.703 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124903009	XR_007063445.1	n.35+344A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000257548	ENST00000547679.1	n.127+344A>G		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.504 AC: 76447 AN: 151764 Hom.: 20223 Cov.: 30

Gnomad AFR AF: 0.337

Gnomad AMI AF: 0.471

Gnomad AMR AF: 0.590

Gnomad ASJ AF: 0.478

Gnomad EAS AF: 0.723

Gnomad SAS AF: 0.576

Gnomad FIN AF: 0.512

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.564

Gnomad OTH AF: 0.520

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

GnomAD4 genome AF: 0.504 AC: 76520 AN: 151882 Hom.: 20248 Cov.: 30 AF XY: 0.508 AC XY: 37689 AN XY: 74208

Gnomad4 AFR AF: 0.337

Gnomad4 AMR AF: 0.591

Gnomad4 ASJ AF: 0.478

Gnomad4 EAS AF: 0.723

Gnomad4 SAS AF: 0.577

Gnomad4 FIN AF: 0.512

Gnomad4 NFE AF: 0.564

Gnomad4 OTH AF: 0.519

Alfa AF: 0.550 Hom.: 25867

Bravo AF: 0.503

Asia WGS AF: 0.608 AC: 2114 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.7
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10861704; hg19: chr12-107491592;