ENST00000567103.2:n.301+51135T>C

Variant names:

• chr16-8061288-A-G
• rs3112666
• ENST00000567103.2:n.301+51135T>C

Variant summary

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

The ENST00000567103.2(ENSG00000260289):​n.301+51135T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.937 in 152,148 control chromosomes in the GnomAD database, including 66,725 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 0.94 (66725 hom., cov: 31)
• Consequence: ENSG00000260289 ENST00000567103.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.34
• Publications: 1 publications found

Genes affected

ENSG00000260289 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.94 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000567103.2. 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
	LOC105371069	NR_197430.1		n.334+51135T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000260289	ENST00000567103.2	TSL:5	n.301+51135T>C		intron	N/A
	ENSG00000260289	ENST00000654046.1		n.334+51135T>C		intron	N/A
	ENSG00000260289	ENST00000670665.1		n.334+51135T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.937 AC: 142394 AN: 152030 Hom.: 66668 Cov.: 31

Gnomad AFR AF: 0.923

Gnomad AMI AF: 0.965

Gnomad AMR AF: 0.952

Gnomad ASJ AF: 0.932

Gnomad EAS AF: 0.903

Gnomad SAS AF: 0.907

Gnomad FIN AF: 0.937

Gnomad MID AF: 0.952

Gnomad NFE AF: 0.946

Gnomad OTH AF: 0.942

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

GnomAD4 genome AF: 0.937 AC: 142510 AN: 152148 Hom.: 66725 Cov.: 31 AF XY: 0.936 AC XY: 69603 AN XY: 74374

African (AFR) AF: 0.923 AC: 38318 AN: 41526

American (AMR) AF: 0.952 AC: 14558 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.932 AC: 3236 AN: 3472

East Asian (EAS) AF: 0.904 AC: 4682 AN: 5180

South Asian (SAS) AF: 0.907 AC: 4366 AN: 4814

European-Finnish (FIN) AF: 0.937 AC: 9876 AN: 10540

Middle Eastern (MID) AF: 0.945 AC: 276 AN: 292

European-Non Finnish (NFE) AF: 0.946 AC: 64330 AN: 68018

Other (OTH) AF: 0.942 AC: 1988 AN: 2110

Alfa AF: 0.939 Hom.: 45287

Bravo AF: 0.937

Asia WGS AF: 0.916 AC: 3184 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.85
DANN	Benign	0.33
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs3112666; hg19: chr16-8111290;