ENST00000547679.1:n.128-3582G>T

Variant names:

• chr12-107118391-G-T
• rs10507216
• ENST00000547679.1:n.128-3582G>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000547679.1(ENSG00000257548):​n.128-3582G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.173 in 152,182 control chromosomes in the GnomAD database, including 2,399 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 0.17 (2399 hom., cov: 32)
• Consequence: ENSG00000257548 ENST00000547679.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.115
• Publications: 4 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=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.281 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000257548	ENST00000547679.1	TSL:3	n.128-3582G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.173 AC: 26328 AN: 152064 Hom.: 2390 Cov.: 32

Gnomad AFR AF: 0.145

Gnomad AMI AF: 0.111

Gnomad AMR AF: 0.154

Gnomad ASJ AF: 0.110

Gnomad EAS AF: 0.295

Gnomad SAS AF: 0.193

Gnomad FIN AF: 0.157

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.190

Gnomad OTH AF: 0.176

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

GnomAD4 genome AF: 0.173 AC: 26366 AN: 152182 Hom.: 2399 Cov.: 32 AF XY: 0.174 AC XY: 12933 AN XY: 74382

African (AFR) AF: 0.146 AC: 6061 AN: 41530

American (AMR) AF: 0.153 AC: 2346 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.110 AC: 381 AN: 3468

East Asian (EAS) AF: 0.294 AC: 1516 AN: 5162

South Asian (SAS) AF: 0.193 AC: 931 AN: 4820

European-Finnish (FIN) AF: 0.157 AC: 1662 AN: 10592

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.190 AC: 12927 AN: 67996

Other (OTH) AF: 0.181 AC: 381 AN: 2110

Alfa AF: 0.167 Hom.: 1388

Bravo AF: 0.171

Asia WGS AF: 0.264 AC: 918 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	9.7
DANN	Benign	0.76
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs10507216; hg19: chr12-107512169;