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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000747510.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000297369	ENST00000747510.1		n.118-12364A>G		intron	N/A
	ENSG00000297369	ENST00000747511.1		n.362-12364A>G		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10879537;

hg19: chr12-73423998;