rs17329620

Variant names:

• chr12-87757000-A-C
• rs17329620
• ENST00000841431.1:n.132+26234T>G

Your query was ambiguous. Multiple possible variants found:

• chr12-87757000-A-C
• chr12-87757000-A-G

Variant summary

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

The ENST00000841431.1(ENSG00000293096):​n.132+26234T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.111 in 152,232 control chromosomes in the GnomAD database, including 1,026 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 0.11 (1026 hom., cov: 32)
• Consequence: ENSG00000293096 ENST00000841431.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0200
• Publications: 1 publications found

Genes affected

ENSG00000293096 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.15 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000841431.1. 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
	ENSG00000293096	ENST00000841431.1		n.132+26234T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.111 AC: 16925 AN: 152114 Hom.: 1020 Cov.: 32

Gnomad AFR AF: 0.0751

Gnomad AMI AF: 0.0461

Gnomad AMR AF: 0.155

Gnomad ASJ AF: 0.116

Gnomad EAS AF: 0.0417

Gnomad SAS AF: 0.109

Gnomad FIN AF: 0.139

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.126

Gnomad OTH AF: 0.103

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

GnomAD4 genome AF: 0.111 AC: 16951 AN: 152232 Hom.: 1026 Cov.: 32 AF XY: 0.114 AC XY: 8490 AN XY: 74412

African (AFR) AF: 0.0752 AC: 3126 AN: 41560

American (AMR) AF: 0.155 AC: 2366 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.116 AC: 402 AN: 3468

East Asian (EAS) AF: 0.0415 AC: 214 AN: 5162

South Asian (SAS) AF: 0.108 AC: 523 AN: 4828

European-Finnish (FIN) AF: 0.139 AC: 1467 AN: 10592

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.126 AC: 8563 AN: 68008

Other (OTH) AF: 0.108 AC: 228 AN: 2114

Alfa AF: 0.0815 Hom.: 144

Bravo AF: 0.109

Asia WGS AF: 0.153 AC: 529 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.6
DANN	Benign	0.41
PhyloP100		-0.020

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs17329620;

hg19: chr12-88150777;