rs17192114

Positions:

• chr12-89777661-T-G

Variant summary

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

The ENST00000651272.1(ENSG00000258216):​n.360-23300T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.118 in 152,260 control chromosomes in the GnomAD database, including 1,393 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 0.12 (1393 hom., cov: 32)
• Consequence: ENSG00000258216 ENST00000651272.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.31

Genes affected

ENSG00000258216 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.156 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107984543	XR_007063399.1	n.171-23300T>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000258216	ENST00000651272.1	n.360-23300T>G		intron_variant

Frequencies

GnomAD3 genomes AF: 0.118 AC: 17941 AN: 152142 Hom.: 1390 Cov.: 32

Gnomad AFR AF: 0.0276

Gnomad AMI AF: 0.175

Gnomad AMR AF: 0.151

Gnomad ASJ AF: 0.169

Gnomad EAS AF: 0.0381

Gnomad SAS AF: 0.0842

Gnomad FIN AF: 0.190

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.159

Gnomad OTH AF: 0.133

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

GnomAD4 genome AF: 0.118 AC: 17944 AN: 152260 Hom.: 1393 Cov.: 32 AF XY: 0.120 AC XY: 8904 AN XY: 74444

Gnomad4 AFR AF: 0.0276

Gnomad4 AMR AF: 0.151

Gnomad4 ASJ AF: 0.169

Gnomad4 EAS AF: 0.0384

Gnomad4 SAS AF: 0.0837

Gnomad4 FIN AF: 0.190

Gnomad4 NFE AF: 0.159

Gnomad4 OTH AF: 0.131

Alfa AF: 0.147 Hom.: 468

Bravo AF: 0.111

Asia WGS AF: 0.0600 AC: 210 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.4
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17192114; hg19: chr12-90171438;