12-4889370-C-G

Variant names:

• chr12-4889370-C-G
• rs11063387
• ENST00000810774.1:n.1509-7546G>C

Variant summary

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

The ENST00000810774.1(ENSG00000287835):​n.1509-7546G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.105 in 151,748 control chromosomes in the GnomAD database, including 1,238 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 0.11 (1238 hom., cov: 33)
• Consequence: ENSG00000287835 ENST00000810774.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.565
• Publications: 1 publications found

Genes affected

ENSG00000287835 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.209 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000810774.1. 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
	ENSG00000287835	ENST00000810774.1		n.1509-7546G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.105 AC: 15977 AN: 151632 Hom.: 1233 Cov.: 33

Gnomad AFR AF: 0.213

Gnomad AMI AF: 0.0440

Gnomad AMR AF: 0.114

Gnomad ASJ AF: 0.0632

Gnomad EAS AF: 0.191

Gnomad SAS AF: 0.0459

Gnomad FIN AF: 0.0991

Gnomad MID AF: 0.0609

Gnomad NFE AF: 0.0400

Gnomad OTH AF: 0.0964

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

GnomAD4 genome AF: 0.105 AC: 16007 AN: 151748 Hom.: 1238 Cov.: 33 AF XY: 0.108 AC XY: 8003 AN XY: 74168

African (AFR) AF: 0.213 AC: 8818 AN: 41368

American (AMR) AF: 0.114 AC: 1742 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.0632 AC: 219 AN: 3464

East Asian (EAS) AF: 0.191 AC: 988 AN: 5172

South Asian (SAS) AF: 0.0459 AC: 220 AN: 4790

European-Finnish (FIN) AF: 0.0991 AC: 1043 AN: 10524

Middle Eastern (MID) AF: 0.0552 AC: 16 AN: 290

European-Non Finnish (NFE) AF: 0.0400 AC: 2717 AN: 67860

Other (OTH) AF: 0.0968 AC: 204 AN: 2108

Alfa AF: 0.0754 Hom.: 104

Bravo AF: 0.111

Asia WGS AF: 0.140 AC: 484 AN: 3452

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.55
DANN	Benign	0.60
PhyloP100		-0.56

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: rs11063387;

hg19: chr12-4998536;