rs12709669

Positions:

• chr18-22227108-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000578741.1(ENSG00000264825):​n.224-779T>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.56 in 152,104 control chromosomes in the GnomAD database, including 24,203 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 0.56 (24203 hom., cov: 33)
• Consequence: ENST00000578741.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.11

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.621 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105372017	XR_935279.3	n.325-8891T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000578741.1	n.224-779T>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.560 AC: 85147 AN: 151988 Hom.: 24170 Cov.: 33

Gnomad AFR AF: 0.627

Gnomad AMI AF: 0.499

Gnomad AMR AF: 0.578

Gnomad ASJ AF: 0.518

Gnomad EAS AF: 0.437

Gnomad SAS AF: 0.539

Gnomad FIN AF: 0.503

Gnomad MID AF: 0.598

Gnomad NFE AF: 0.539

Gnomad OTH AF: 0.549

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

GnomAD4 genome AF: 0.560 AC: 85241 AN: 152104 Hom.: 24203 Cov.: 33 AF XY: 0.558 AC XY: 41513 AN XY: 74360

Gnomad4 AFR AF: 0.627

Gnomad4 AMR AF: 0.578

Gnomad4 ASJ AF: 0.518

Gnomad4 EAS AF: 0.437

Gnomad4 SAS AF: 0.539

Gnomad4 FIN AF: 0.503

Gnomad4 NFE AF: 0.539

Gnomad4 OTH AF: 0.546

Alfa AF: 0.570 Hom.: 4676

Bravo AF: 0.571

Asia WGS AF: 0.481 AC: 1675 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	13
DANN	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12709669; hg19: chr18-19807071;