rs12231166

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr12-100177240-A-C
• chr12-100177240-A-T

Variant summary

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

The ENST00000546397.1(ENSG00000290576):​n.85-120T>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 ENST00000546397.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.527
• Publications: 3 publications found

Genes affected

ENSG00000290576 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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	ENST00000548404.7	n.967-120T>G		intron_variant	Intron 5 of 12	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

African (AFR) AF: 0.0300 AC: 82 AN: 2734

American (AMR) AF: 0.233 AC: 639 AN: 2742

Ashkenazi Jewish (ASJ) AF: 0.134 AC: 502 AN: 3748

East Asian (EAS) AF: 0.558 AC: 3113 AN: 5576

South Asian (SAS) AF: 0.264 AC: 3515 AN: 13290

European-Finnish (FIN) AF: 0.191 AC: 1017 AN: 5338

Middle Eastern (MID) AF: 0.110 AC: 57 AN: 518

European-Non Finnish (NFE) AF: 0.124 AC: 8873 AN: 71508

Other (OTH) AF: 0.154 AC: 1059 AN: 6882

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

African (AFR) AF: 0.0281 AC: 1167 AN: 41516

American (AMR) AF: 0.244 AC: 3726 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.149 AC: 517 AN: 3470

East Asian (EAS) AF: 0.588 AC: 3016 AN: 5130

South Asian (SAS) AF: 0.328 AC: 1578 AN: 4808

European-Finnish (FIN) AF: 0.226 AC: 2369 AN: 10498

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.135 AC: 9198 AN: 67946

Other (OTH) AF: 0.157 AC: 331 AN: 2110

Alfa AF: 0.137 Hom.: 883

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
PhyloP100		0.53

Splicing

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

Other links and lift over

dbSNP: rs12231166; hg19: chr12-100571018; COSMIC: COSV107248796;