12-68805965-T-G

Variant names:

• chr12-68805965-T-G
• rs1144943
• ENST00000686859.2:n.1093T>G

Variant summary

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

The ENST00000686859.2(ENSG00000289595):​n.1093T>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.408 in 151,406 control chromosomes in the GnomAD database, including 13,057 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 0.41 (13057 hom., cov: 29)
• Consequence: ENSG00000289595 ENST00000686859.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.32
• Publications: 13 publications found

Genes affected

ENSG00000289595 (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 = 0.462 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000686859.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000289595	ENST00000686859.2		n.1093T>G		non_coding_transcript_exon	Exon 1 of 1

Frequencies

GnomAD3 genomes AF: 0.408 AC: 61684 AN: 151288 Hom.: 13031 Cov.: 29

Gnomad AFR AF: 0.467

Gnomad AMI AF: 0.521

Gnomad AMR AF: 0.268

Gnomad ASJ AF: 0.300

Gnomad EAS AF: 0.280

Gnomad SAS AF: 0.249

Gnomad FIN AF: 0.441

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.424

Gnomad OTH AF: 0.376

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

GnomAD4 genome AF: 0.408 AC: 61769 AN: 151406 Hom.: 13057 Cov.: 29 AF XY: 0.401 AC XY: 29671 AN XY: 73984

African (AFR) AF: 0.467 AC: 19259 AN: 41206

American (AMR) AF: 0.268 AC: 4067 AN: 15158

Ashkenazi Jewish (ASJ) AF: 0.300 AC: 1039 AN: 3464

East Asian (EAS) AF: 0.281 AC: 1446 AN: 5146

South Asian (SAS) AF: 0.247 AC: 1188 AN: 4806

European-Finnish (FIN) AF: 0.441 AC: 4615 AN: 10468

Middle Eastern (MID) AF: 0.299 AC: 88 AN: 294

European-Non Finnish (NFE) AF: 0.424 AC: 28807 AN: 67864

Other (OTH) AF: 0.376 AC: 785 AN: 2088

Alfa AF: 0.412 Hom.: 49305

Bravo AF: 0.399

Asia WGS AF: 0.296 AC: 1026 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.50
DANN	Benign	0.45
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs1144943; hg19: chr12-69199745;