rs17459885

Positions:

• chr12-30207946-T-C

Variant summary

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

The ENST00000549055.1(ENSG00000257262):​n.127-496T>C 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 0.105 in 152,282 control chromosomes in the GnomAD database, including 1,000 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 0.10 (1000 hom., cov: 33)
• Consequence: ENST00000549055.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.154

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.137 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000549055.1	n.127-496T>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.105 AC: 15952 AN: 152164 Hom.: 1000 Cov.: 33

Gnomad AFR AF: 0.0423

Gnomad AMI AF: 0.179

Gnomad AMR AF: 0.103

Gnomad ASJ AF: 0.0926

Gnomad EAS AF: 0.129

Gnomad SAS AF: 0.0358

Gnomad FIN AF: 0.143

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.140

Gnomad OTH AF: 0.125

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

GnomAD4 genome AF: 0.105 AC: 15949 AN: 152282 Hom.: 1000 Cov.: 33 AF XY: 0.103 AC XY: 7660 AN XY: 74460

Gnomad4 AFR AF: 0.0422

Gnomad4 AMR AF: 0.103

Gnomad4 ASJ AF: 0.0926

Gnomad4 EAS AF: 0.129

Gnomad4 SAS AF: 0.0358

Gnomad4 FIN AF: 0.143

Gnomad4 NFE AF: 0.140

Gnomad4 OTH AF: 0.125

Alfa AF: 0.111 Hom.: 132

Bravo AF: 0.102

Asia WGS AF: 0.0830 AC: 286 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.7
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17459885; hg19: chr12-30360879;