rs17126180

Variant names:

• chr12-51870172-C-G
• rs17126180
• ENST00000759510.1:n.65+487G>C

Your query was ambiguous. Multiple possible variants found:

• chr12-51870172-C-G
• chr12-51870172-C-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000759510.1(ENSG00000298968):​n.65+487G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0807 in 152,154 control chromosomes in the GnomAD database, including 716 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 0.081 (716 hom., cov: 32)
• Consequence: ENSG00000298968 ENST00000759510.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0410
• Publications: 7 publications found

Genes affected

ENSG00000298968 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.175 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000298968	ENST00000759510.1	n.65+487G>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0806 AC: 12258 AN: 152036 Hom.: 710 Cov.: 32

Gnomad AFR AF: 0.0528

Gnomad AMI AF: 0.0474

Gnomad AMR AF: 0.176

Gnomad ASJ AF: 0.100

Gnomad EAS AF: 0.185

Gnomad SAS AF: 0.167

Gnomad FIN AF: 0.132

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0537

Gnomad OTH AF: 0.0810

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

GnomAD4 genome AF: 0.0807 AC: 12279 AN: 152154 Hom.: 716 Cov.: 32 AF XY: 0.0881 AC XY: 6551 AN XY: 74372

African (AFR) AF: 0.0531 AC: 2204 AN: 41530

American (AMR) AF: 0.175 AC: 2678 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.100 AC: 348 AN: 3470

East Asian (EAS) AF: 0.185 AC: 956 AN: 5170

South Asian (SAS) AF: 0.167 AC: 806 AN: 4812

European-Finnish (FIN) AF: 0.132 AC: 1397 AN: 10586

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.0537 AC: 3654 AN: 68012

Other (OTH) AF: 0.0825 AC: 174 AN: 2108

Alfa AF: 0.0562 Hom.: 195

Bravo AF: 0.0837

Asia WGS AF: 0.180 AC: 627 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	0.72
DANN	Benign	0.54
PhyloP100		0.041

Splicing

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

Other links and lift over

dbSNP: rs17126180; hg19: chr12-52263956;