rs1144943

Positions:

• chr12-68805965-T-G

Variant summary

Our verdict is Benign. Variant got -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: ENST00000686859.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.32

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000686859.2	n.1093T>G		non_coding_transcript_exon_variant	1/1

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

Gnomad4 AFR AF: 0.467

Gnomad4 AMR AF: 0.268

Gnomad4 ASJ AF: 0.300

Gnomad4 EAS AF: 0.281

Gnomad4 SAS AF: 0.247

Gnomad4 FIN AF: 0.441

Gnomad4 NFE AF: 0.424

Gnomad4 OTH AF: 0.376

Alfa AF: 0.405 Hom.: 20334

Bravo AF: 0.399

Asia WGS AF: 0.296 AC: 1026 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	0.50
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1144943; hg19: chr12-69199745;