12-107103535-C-T

Variant names:

• chr12-107103535-C-T
• rs7297614
• ENST00000547679.1:n.127+6065C>T

Variant summary

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

The ENST00000547679.1(ENSG00000257548):​n.127+6065C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.694 in 151,868 control chromosomes in the GnomAD database, including 37,453 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 0.69 (37453 hom., cov: 30)
• Consequence: ENSG00000257548 ENST00000547679.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00400

Genes affected

ENSG00000257548 (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 (EAS) allele frequency at 95% confidence interval = 0.946 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
ENSG00000257548	ENST00000547679.1	n.127+6065C>T		intron_variant	Intron 2 of 3	3

Frequencies

GnomAD3 genomes AF: 0.694 AC: 105327 AN: 151750 Hom.: 37392 Cov.: 30

Gnomad AFR AF: 0.798

Gnomad AMI AF: 0.511

Gnomad AMR AF: 0.760

Gnomad ASJ AF: 0.551

Gnomad EAS AF: 0.968

Gnomad SAS AF: 0.713

Gnomad FIN AF: 0.580

Gnomad MID AF: 0.639

Gnomad NFE AF: 0.622

Gnomad OTH AF: 0.678

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

GnomAD4 genome AF: 0.694 AC: 105456 AN: 151868 Hom.: 37453 Cov.: 30 AF XY: 0.697 AC XY: 51739 AN XY: 74196

Gnomad4 AFR AF: 0.798

Gnomad4 AMR AF: 0.761

Gnomad4 ASJ AF: 0.551

Gnomad4 EAS AF: 0.968

Gnomad4 SAS AF: 0.714

Gnomad4 FIN AF: 0.580

Gnomad4 NFE AF: 0.622

Gnomad4 OTH AF: 0.679

Alfa AF: 0.639 Hom.: 14281

Bravo AF: 0.713

Asia WGS AF: 0.835 AC: 2901 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.71
DANN	Benign	0.14

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7297614; hg19: chr12-107497313;