rs10879537

Variant names:

• chr12-73030218-A-G
• rs10879537
• ENST00000747510.1:n.118-12364A>G

Your query was ambiguous. Multiple possible variants found:

• chr12-73030218-A-G
• chr12-73030218-A-T

Variant summary

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

The ENST00000747510.1(ENSG00000297369):​n.118-12364A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.717 in 151,844 control chromosomes in the GnomAD database, including 39,293 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 0.72 (39293 hom., cov: 31)
• Consequence: ENSG00000297369 ENST00000747510.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.39
• Publications: 0 publications found

Genes affected

ENSG00000297369 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.728 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105369838	XR_945088.2	n.578-12364A>G		intron_variant	Intron 6 of 6
LOC105369838	XR_945089.2	n.527-12364A>G		intron_variant	Intron 5 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000297369	ENST00000747510.1	n.118-12364A>G		intron_variant	Intron 1 of 2
ENSG00000297369	ENST00000747511.1	n.362-12364A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.717 AC: 108720 AN: 151728 Hom.: 39243 Cov.: 31

Gnomad AFR AF: 0.729

Gnomad AMI AF: 0.693

Gnomad AMR AF: 0.665

Gnomad ASJ AF: 0.694

Gnomad EAS AF: 0.505

Gnomad SAS AF: 0.730

Gnomad FIN AF: 0.738

Gnomad MID AF: 0.750

Gnomad NFE AF: 0.734

Gnomad OTH AF: 0.702

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

GnomAD4 genome AF: 0.717 AC: 108822 AN: 151844 Hom.: 39293 Cov.: 31 AF XY: 0.715 AC XY: 53071 AN XY: 74204

African (AFR) AF: 0.730 AC: 30225 AN: 41408

American (AMR) AF: 0.665 AC: 10134 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.694 AC: 2407 AN: 3468

East Asian (EAS) AF: 0.505 AC: 2588 AN: 5124

South Asian (SAS) AF: 0.730 AC: 3507 AN: 4804

European-Finnish (FIN) AF: 0.738 AC: 7804 AN: 10570

Middle Eastern (MID) AF: 0.745 AC: 216 AN: 290

European-Non Finnish (NFE) AF: 0.734 AC: 49829 AN: 67920

Other (OTH) AF: 0.701 AC: 1480 AN: 2110

Alfa AF: 0.717 Hom.: 53608

Bravo AF: 0.708

Asia WGS AF: 0.630 AC: 2193 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.056
DANN	Benign	0.39
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs10879537; hg19: chr12-73423998;