rs9286879

chr1-172893094-A-G

Variant summary

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

The ENST00000432694.2(ENSG00000224228):n.224-111188A>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 0.33 in 152,070 control chromosomes in the GnomAD database, including 9,737 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 0.33 (9737 hom., cov: 32)
• Consequence: ENST00000432694.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.649

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.874 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
	ENST00000432694.2	n.224-111188A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.330 AC: 50153 AN: 151950 Hom.: 9731 Cov.: 32

Gnomad AFR AF: 0.365

Gnomad AMI AF: 0.138

Gnomad AMR AF: 0.467

Gnomad ASJ AF: 0.263

Gnomad EAS AF: 0.896

Gnomad SAS AF: 0.417

Gnomad FIN AF: 0.296

Gnomad MID AF: 0.364

Gnomad NFE AF: 0.240

Gnomad OTH AF: 0.334

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

GnomAD4 genome AF: 0.330 AC: 50178 AN: 152070 Hom.: 9737 Cov.: 32 AF XY: 0.338 AC XY: 25135 AN XY: 74312

Gnomad4 AFR AF: 0.365

Gnomad4 AMR AF: 0.467

Gnomad4 ASJ AF: 0.263

Gnomad4 EAS AF: 0.896

Gnomad4 SAS AF: 0.417

Gnomad4 FIN AF: 0.296

Gnomad4 NFE AF: 0.240

Gnomad4 OTH AF: 0.332

Alfa AF: 0.275 Hom.: 15694

Bravo AF: 0.354

Asia WGS AF: 0.560 AC: 1949 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	5.6
Dann	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9286879; hg19: chr1-172862234;