12-4887885-C-T

Variant names:

• chr12-4887885-C-T
• rs11063385
• ENST00000810774.1:n.1509-6061G>A

Variant summary

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

The ENST00000810774.1(ENSG00000287835):​n.1509-6061G>A 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 152,024 control chromosomes in the GnomAD database, including 1,232 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 0.10 (1232 hom., cov: 33)
• Consequence: ENSG00000287835 ENST00000810774.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.424
• 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.1509-6061G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.105 AC: 15911 AN: 151908 Hom.: 1226 Cov.: 33

Gnomad AFR AF: 0.213

Gnomad AMI AF: 0.0439

Gnomad AMR AF: 0.114

Gnomad ASJ AF: 0.0634

Gnomad EAS AF: 0.189

Gnomad SAS AF: 0.0457

Gnomad FIN AF: 0.0937

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0398

Gnomad OTH AF: 0.0966

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

GnomAD4 genome AF: 0.105 AC: 15943 AN: 152024 Hom.: 1232 Cov.: 33 AF XY: 0.107 AC XY: 7961 AN XY: 74324

African (AFR) AF: 0.213 AC: 8822 AN: 41440

American (AMR) AF: 0.114 AC: 1741 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.0634 AC: 220 AN: 3468

East Asian (EAS) AF: 0.189 AC: 979 AN: 5168

South Asian (SAS) AF: 0.0457 AC: 220 AN: 4814

European-Finnish (FIN) AF: 0.0937 AC: 990 AN: 10568

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.0399 AC: 2710 AN: 67972

Other (OTH) AF: 0.0970 AC: 205 AN: 2114

Alfa AF: 0.0193 Hom.: 15

Bravo AF: 0.111

Asia WGS AF: 0.138 AC: 480 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.88
DANN	Benign	0.41
PhyloP100		-0.42

Splicing

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

Other links and lift over

dbSNP: rs11063385; hg19: chr12-4997051;