rs9669515

chr12-30216329-A-Gchr12-30216329-A-T

Variant summary

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

The ENST00000549055.1(ENSG00000257262):n.258-1274A>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 0.766 in 152,140 control chromosomes in the GnomAD database, including 45,223 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 0.77 (45223 hom., cov: 32)
• Consequence: ENST00000549055.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.515

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.892 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
	ENST00000549055.1	n.258-1274A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.765 AC: 116338 AN: 152020 Hom.: 45151 Cov.: 32

Gnomad AFR AF: 0.900

Gnomad AMI AF: 0.768

Gnomad AMR AF: 0.772

Gnomad ASJ AF: 0.715

Gnomad EAS AF: 0.830

Gnomad SAS AF: 0.734

Gnomad FIN AF: 0.678

Gnomad MID AF: 0.748

Gnomad NFE AF: 0.695

Gnomad OTH AF: 0.755

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

GnomAD4 genome AF: 0.766 AC: 116473 AN: 152140 Hom.: 45223 Cov.: 32 AF XY: 0.764 AC XY: 56823 AN XY: 74356

Gnomad4 AFR AF: 0.900

Gnomad4 AMR AF: 0.773

Gnomad4 ASJ AF: 0.715

Gnomad4 EAS AF: 0.831

Gnomad4 SAS AF: 0.734

Gnomad4 FIN AF: 0.678

Gnomad4 NFE AF: 0.695

Gnomad4 OTH AF: 0.758

Alfa AF: 0.682 Hom.: 6236

Bravo AF: 0.779

Asia WGS AF: 0.799 AC: 2776 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	2.1
Dann	Benign	0.23

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9669515; hg19: chr12-30369262;