rs12829697

Variant names:

• chr12-30023023-A-G
• rs12829697
• ENST00000801042.1:n.145-9093T>C

Your query was ambiguous. Multiple possible variants found:

• chr12-30023023-A-G
• chr12-30023023-A-T

Variant summary

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

The ENST00000801042.1(ENSG00000304211):​n.145-9093T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.102 in 152,212 control chromosomes in the GnomAD database, including 1,055 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 0.10 (1055 hom., cov: 32)
• Consequence: ENSG00000304211 ENST00000801042.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.654
• Publications: 1 publications found

Genes affected

ENSG00000304211 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.23 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105369715	XR_001749060.1	n.135-9093T>C		intron_variant	Intron 2 of 5
LOC105369715	XR_001749061.1	n.135-9093T>C		intron_variant	Intron 2 of 4
LOC105369715	XR_931474.1	n.135-9093T>C		intron_variant	Intron 2 of 4
LOC105369715	XR_931476.1	n.135-9093T>C		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000304211	ENST00000801042.1	n.145-9093T>C		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.102 AC: 15508 AN: 152094 Hom.: 1055 Cov.: 32

Gnomad AFR AF: 0.0227

Gnomad AMI AF: 0.149

Gnomad AMR AF: 0.122

Gnomad ASJ AF: 0.0934

Gnomad EAS AF: 0.242

Gnomad SAS AF: 0.165

Gnomad FIN AF: 0.144

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.124

Gnomad OTH AF: 0.113

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

GnomAD4 genome AF: 0.102 AC: 15505 AN: 152212 Hom.: 1055 Cov.: 32 AF XY: 0.104 AC XY: 7727 AN XY: 74412

African (AFR) AF: 0.0227 AC: 942 AN: 41568

American (AMR) AF: 0.122 AC: 1862 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.0934 AC: 324 AN: 3470

East Asian (EAS) AF: 0.242 AC: 1247 AN: 5162

South Asian (SAS) AF: 0.164 AC: 791 AN: 4824

European-Finnish (FIN) AF: 0.144 AC: 1527 AN: 10598

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.124 AC: 8422 AN: 68002

Other (OTH) AF: 0.112 AC: 236 AN: 2114

Alfa AF: 0.105 Hom.: 153

Bravo AF: 0.0986

Asia WGS AF: 0.168 AC: 583 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	6.8
DANN	Benign	0.86
PhyloP100		0.65

Splicing

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

Other links and lift over

dbSNP: rs12829697; hg19: chr12-30175956;