12-111766623-A-G

Variant names:

• chr12-111766623-A-G
• rs886205
• ENST00000546840.3:c.102+10878A>G

Variant summary

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

The ENST00000546840.3(ENSG00000257767):​c.102+10878A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.355 in 152,094 control chromosomes in the GnomAD database, including 14,025 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 0.35 (14025 hom., cov: 33)
• Consequence: ENSG00000257767 ENST00000546840.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.350
• Publications: 66 publications found

Genes affected

ENSG00000257767 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.836 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000546840.3. 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
	ENSG00000257767	ENST00000546840.3	TSL:5	c.102+10878A>G		intron	N/A	ENSP00000450353.4	F8VP50

Frequencies

GnomAD3 genomes AF: 0.354 AC: 53849 AN: 151976 Hom.: 13985 Cov.: 33

Gnomad AFR AF: 0.680

Gnomad AMI AF: 0.146

Gnomad AMR AF: 0.329

Gnomad ASJ AF: 0.0998

Gnomad EAS AF: 0.857

Gnomad SAS AF: 0.318

Gnomad FIN AF: 0.154

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.174

Gnomad OTH AF: 0.335

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

GnomAD4 genome AF: 0.355 AC: 53950 AN: 152094 Hom.: 14025 Cov.: 33 AF XY: 0.355 AC XY: 26369 AN XY: 74354

African (AFR) AF: 0.680 AC: 28239 AN: 41498

American (AMR) AF: 0.329 AC: 5026 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0998 AC: 346 AN: 3466

East Asian (EAS) AF: 0.857 AC: 4413 AN: 5150

South Asian (SAS) AF: 0.317 AC: 1530 AN: 4820

European-Finnish (FIN) AF: 0.154 AC: 1633 AN: 10598

Middle Eastern (MID) AF: 0.353 AC: 103 AN: 292

European-Non Finnish (NFE) AF: 0.174 AC: 11829 AN: 67976

Other (OTH) AF: 0.331 AC: 698 AN: 2108

Alfa AF: 0.273 Hom.: 12051

Bravo AF: 0.388

Asia WGS AF: 0.533 AC: 1852 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.6
DANN	Benign	0.51
PhyloP100		-0.35
PromoterAI		-0.0093	Neutral

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs886205; hg19: chr12-112204427;