12-107103535-C-T

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 15 publications found

Genes affected

ENSG00000257548 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000547679.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000257548	ENST00000547679.1	TSL:3	n.127+6065C>T		intron	N/A

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

African (AFR) AF: 0.798 AC: 33034 AN: 41372

American (AMR) AF: 0.761 AC: 11599 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.551 AC: 1912 AN: 3470

East Asian (EAS) AF: 0.968 AC: 5013 AN: 5178

South Asian (SAS) AF: 0.714 AC: 3438 AN: 4812

European-Finnish (FIN) AF: 0.580 AC: 6100 AN: 10512

Middle Eastern (MID) AF: 0.660 AC: 194 AN: 294

European-Non Finnish (NFE) AF: 0.622 AC: 42266 AN: 67958

Other (OTH) AF: 0.679 AC: 1435 AN: 2112

Alfa AF: 0.639 Hom.: 16061

Bravo AF: 0.713

Asia WGS AF: 0.835 AC: 2901 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.71
DANN	Benign	0.14
PhyloP100		-0.0040

Splicing

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

Other links and lift over

dbSNP: rs7297614; hg19: chr12-107497313;