12-114438804-T-C

Variant names:

• chr12-114438804-T-C
• rs933739
• ENST00000835971.1:n.318+9693A>G

Variant summary

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

The ENST00000835971.1(ENSG00000289101):​n.318+9693A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.342 in 137,010 control chromosomes in the GnomAD database, including 8,850 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 0.34 (8850 hom., cov: 27)
• Consequence: ENSG00000289101 ENST00000835971.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.620
• Publications: 1 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=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.447 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000835971.1. 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
	ENSG00000289101	ENST00000835971.1		n.318+9693A>G		intron	N/A
	ENSG00000289101	ENST00000835972.1		n.288-5811A>G		intron	N/A
	ENSG00000289101	ENST00000835973.1		n.287+9693A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.342 AC: 46827 AN: 136948 Hom.: 8854 Cov.: 27

Gnomad AFR AF: 0.161

Gnomad AMI AF: 0.507

Gnomad AMR AF: 0.335

Gnomad ASJ AF: 0.409

Gnomad EAS AF: 0.0171

Gnomad SAS AF: 0.270

Gnomad FIN AF: 0.395

Gnomad MID AF: 0.504

Gnomad NFE AF: 0.451

Gnomad OTH AF: 0.365

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

GnomAD4 genome AF: 0.342 AC: 46813 AN: 137010 Hom.: 8850 Cov.: 27 AF XY: 0.338 AC XY: 22296 AN XY: 65946

African (AFR) AF: 0.161 AC: 5527 AN: 34336

American (AMR) AF: 0.335 AC: 4466 AN: 13346

Ashkenazi Jewish (ASJ) AF: 0.409 AC: 1383 AN: 3380

East Asian (EAS) AF: 0.0172 AC: 78 AN: 4540

South Asian (SAS) AF: 0.271 AC: 1194 AN: 4410

European-Finnish (FIN) AF: 0.395 AC: 3313 AN: 8392

Middle Eastern (MID) AF: 0.519 AC: 134 AN: 258

European-Non Finnish (NFE) AF: 0.451 AC: 29601 AN: 65612

Other (OTH) AF: 0.362 AC: 677 AN: 1868

Alfa AF: 0.228 Hom.: 652

Bravo AF: 0.300

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.0
DANN	Benign	0.64
PhyloP100		-0.62

Splicing

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

Other links and lift over

dbSNP: rs933739; hg19: chr12-114876609;