12-107105494-T-C

Variant names:

• chr12-107105494-T-C
• rs12315175
• ENST00000547679.1:n.127+8024T>C

Variant summary

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

The ENST00000547679.1(ENSG00000257548):​n.127+8024T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.184 in 151,984 control chromosomes in the GnomAD database, including 2,682 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 0.18 (2682 hom., cov: 31)
• Consequence: ENSG00000257548 ENST00000547679.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.129
• Publications: 22 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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.295 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+8024T>C		intron_variant	Intron 2 of 3	3

Frequencies

GnomAD3 genomes AF: 0.184 AC: 27968 AN: 151866 Hom.: 2672 Cov.: 31

Gnomad AFR AF: 0.153

Gnomad AMI AF: 0.236

Gnomad AMR AF: 0.167

Gnomad ASJ AF: 0.202

Gnomad EAS AF: 0.307

Gnomad SAS AF: 0.0742

Gnomad FIN AF: 0.203

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.201

Gnomad OTH AF: 0.192

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

GnomAD4 genome AF: 0.184 AC: 27988 AN: 151984 Hom.: 2682 Cov.: 31 AF XY: 0.184 AC XY: 13628 AN XY: 74260

African (AFR) AF: 0.153 AC: 6328 AN: 41446

American (AMR) AF: 0.166 AC: 2542 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.202 AC: 699 AN: 3468

East Asian (EAS) AF: 0.308 AC: 1582 AN: 5140

South Asian (SAS) AF: 0.0753 AC: 362 AN: 4810

European-Finnish (FIN) AF: 0.203 AC: 2144 AN: 10554

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.201 AC: 13664 AN: 67980

Other (OTH) AF: 0.191 AC: 402 AN: 2110

Alfa AF: 0.193 Hom.: 6323

Bravo AF: 0.187

Asia WGS AF: 0.190 AC: 661 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.3
DANN	Benign	0.72
PhyloP100		0.13
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs12315175; hg19: chr12-107499272;