chr12-100177240-A-C

Variant names:

• chr12-100177240-A-C
• rs12231166
• ENST00000546397.1:n.85-120T>G

Variant summary

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

The ENST00000548404.6(ENSG00000290576):​n.362-120T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.155 in 264,276 control chromosomes in the GnomAD database, including 5,242 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 0.14 (2636 hom., cov: 32)
  • Exomes 𝑓: 0.17 (2606 hom.)
• Consequence: ENSG00000290576 ENST00000548404.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.527

Genes affected

ENSG00000290576 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.57 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
ENSG00000290576	ENST00000546397.1	n.85-120T>G		intron_variant	Intron 1 of 2	4
ENSG00000290576	ENST00000548404.6	n.362-120T>G		intron_variant	Intron 3 of 4	3
ENSG00000290576	ENST00000550096.5	n.558-120T>G		intron_variant	Intron 3 of 5	3

Frequencies

GnomAD3 genomes AF: 0.145 AC: 22000 AN: 151820 Hom.: 2634 Cov.: 32

Gnomad AFR AF: 0.0282

Gnomad AMI AF: 0.0800

Gnomad AMR AF: 0.243

Gnomad ASJ AF: 0.149

Gnomad EAS AF: 0.588

Gnomad SAS AF: 0.329

Gnomad FIN AF: 0.226

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.135

Gnomad OTH AF: 0.159

GnomAD4 exome AF: 0.168 AC: 18857 AN: 112336 Hom.: 2606 AF XY: 0.174 AC XY: 10761 AN XY: 61700

Gnomad4 AFR exome AF: 0.0300

Gnomad4 AMR exome AF: 0.233

Gnomad4 ASJ exome AF: 0.134

Gnomad4 EAS exome AF: 0.558

Gnomad4 SAS exome AF: 0.264

Gnomad4 FIN exome AF: 0.191

Gnomad4 NFE exome AF: 0.124

Gnomad4 OTH exome AF: 0.154

GnomAD4 genome AF: 0.145 AC: 22001 AN: 151940 Hom.: 2636 Cov.: 32 AF XY: 0.159 AC XY: 11809 AN XY: 74268

Gnomad4 AFR AF: 0.0281

Gnomad4 AMR AF: 0.244

Gnomad4 ASJ AF: 0.149

Gnomad4 EAS AF: 0.588

Gnomad4 SAS AF: 0.328

Gnomad4 FIN AF: 0.226

Gnomad4 NFE AF: 0.135

Gnomad4 OTH AF: 0.157

Alfa AF: 0.0984 Hom.: 237

Bravo AF: 0.139

Asia WGS AF: 0.394 AC: 1369 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	9.4
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12231166; hg19: chr12-100571018;