chr12-71097725-C-T

Variant names:

• chr12-71097725-C-T
• rs11178602
• ENST00000549357.2:n.609+18125G>A

Variant summary

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

The ENST00000549357.2(ENSG00000258053):​n.609+18125G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.33 in 151,924 control chromosomes in the GnomAD database, including 9,032 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 0.33 (9032 hom., cov: 33)
• Consequence: ENSG00000258053 ENST00000549357.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.39
• Publications: 6 publications found

Genes affected

ENSG00000258053 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.412 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000549357.2. 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
	ENSG00000258053	ENST00000549357.2	TSL:1	n.609+18125G>A		intron	N/A
	ENSG00000258053	ENST00000716229.1		n.177+6625G>A		intron	N/A
	ENSG00000258053	ENST00000716230.1		n.516+18125G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.330 AC: 50088 AN: 151806 Hom.: 9028 Cov.: 33

Gnomad AFR AF: 0.196

Gnomad AMI AF: 0.516

Gnomad AMR AF: 0.277

Gnomad ASJ AF: 0.450

Gnomad EAS AF: 0.303

Gnomad SAS AF: 0.288

Gnomad FIN AF: 0.350

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.416

Gnomad OTH AF: 0.351

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

GnomAD4 genome AF: 0.330 AC: 50104 AN: 151924 Hom.: 9032 Cov.: 33 AF XY: 0.325 AC XY: 24162 AN XY: 74242

African (AFR) AF: 0.196 AC: 8123 AN: 41486

American (AMR) AF: 0.276 AC: 4208 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.450 AC: 1561 AN: 3472

East Asian (EAS) AF: 0.304 AC: 1567 AN: 5160

South Asian (SAS) AF: 0.290 AC: 1396 AN: 4814

European-Finnish (FIN) AF: 0.350 AC: 3672 AN: 10504

Middle Eastern (MID) AF: 0.374 AC: 110 AN: 294

European-Non Finnish (NFE) AF: 0.416 AC: 28268 AN: 67962

Other (OTH) AF: 0.348 AC: 729 AN: 2096

Alfa AF: 0.349 Hom.: 1667

Bravo AF: 0.319

Asia WGS AF: 0.270 AC: 934 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.37
DANN	Benign	0.42
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs11178602; hg19: chr12-71491505;