12-114430333-A-G

Variant names:

• chr12-114430333-A-G
• rs1265507
• ENST00000835971.1:n.319-15766T>C

Variant summary

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

The ENST00000835971.1(ENSG00000289101):​n.319-15766T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.514 in 151,874 control chromosomes in the GnomAD database, including 20,595 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 0.51 (20595 hom., cov: 31)
• Consequence: ENSG00000289101 ENST00000835971.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.415
• Publications: 16 publications found

Genes affected

ENSG00000289101 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) 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
LOC105369998	XR_007063469.1	n.86-5256T>C		intron_variant	Intron 1 of 2
LOC105369998	XR_945376.3	n.86-5256T>C		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000289101	ENST00000835971.1	n.319-15766T>C		intron_variant	Intron 1 of 1
ENSG00000289101	ENST00000835972.1	n.538+2410T>C		intron_variant	Intron 2 of 3
ENSG00000289101	ENST00000835973.1	n.288-5256T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.514 AC: 78067 AN: 151756 Hom.: 20581 Cov.: 31

Gnomad AFR AF: 0.576

Gnomad AMI AF: 0.615

Gnomad AMR AF: 0.454

Gnomad ASJ AF: 0.480

Gnomad EAS AF: 0.205

Gnomad SAS AF: 0.355

Gnomad FIN AF: 0.435

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.538

Gnomad OTH AF: 0.501

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

GnomAD4 genome AF: 0.514 AC: 78123 AN: 151874 Hom.: 20595 Cov.: 31 AF XY: 0.505 AC XY: 37459 AN XY: 74206

African (AFR) AF: 0.576 AC: 23859 AN: 41416

American (AMR) AF: 0.453 AC: 6925 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.480 AC: 1661 AN: 3460

East Asian (EAS) AF: 0.205 AC: 1054 AN: 5152

South Asian (SAS) AF: 0.354 AC: 1706 AN: 4814

European-Finnish (FIN) AF: 0.435 AC: 4561 AN: 10484

Middle Eastern (MID) AF: 0.585 AC: 172 AN: 294

European-Non Finnish (NFE) AF: 0.538 AC: 36560 AN: 67958

Other (OTH) AF: 0.505 AC: 1065 AN: 2108

Alfa AF: 0.519 Hom.: 63241

Bravo AF: 0.519

Asia WGS AF: 0.333 AC: 1159 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.25
DANN	Benign	0.57
PhyloP100		-0.41

Splicing

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

Other links and lift over

dbSNP: rs1265507; hg19: chr12-114868138;