ENST00000567103.2:n.302-16692T>G

Variant names:

• chr16-8023916-A-C
• rs1532926
• ENST00000567103.2:n.302-16692T>G

Variant summary

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

The ENST00000567103.2(ENSG00000260289):​n.302-16692T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.342 in 152,010 control chromosomes in the GnomAD database, including 9,294 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 0.34 (9294 hom., cov: 33)
• Consequence: ENSG00000260289 ENST00000567103.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.269
• Publications: 4 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=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.385 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC105371069	NR_197430.1		n.335-16692T>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000260289	ENST00000567103.2	TSL:5	n.302-16692T>G		intron	N/A
	ENSG00000260289	ENST00000654046.1		n.335-16692T>G		intron	N/A
	ENSG00000260289	ENST00000670665.1		n.335-16692T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.342 AC: 51968 AN: 151892 Hom.: 9288 Cov.: 33

Gnomad AFR AF: 0.274

Gnomad AMI AF: 0.447

Gnomad AMR AF: 0.393

Gnomad ASJ AF: 0.424

Gnomad EAS AF: 0.167

Gnomad SAS AF: 0.190

Gnomad FIN AF: 0.360

Gnomad MID AF: 0.318

Gnomad NFE AF: 0.387

Gnomad OTH AF: 0.372

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

GnomAD4 genome AF: 0.342 AC: 52014 AN: 152010 Hom.: 9294 Cov.: 33 AF XY: 0.337 AC XY: 25012 AN XY: 74304

African (AFR) AF: 0.274 AC: 11377 AN: 41468

American (AMR) AF: 0.393 AC: 6000 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.424 AC: 1469 AN: 3462

East Asian (EAS) AF: 0.167 AC: 864 AN: 5174

South Asian (SAS) AF: 0.191 AC: 919 AN: 4818

European-Finnish (FIN) AF: 0.360 AC: 3794 AN: 10550

Middle Eastern (MID) AF: 0.325 AC: 95 AN: 292

European-Non Finnish (NFE) AF: 0.387 AC: 26308 AN: 67978

Other (OTH) AF: 0.370 AC: 780 AN: 2108

Alfa AF: 0.351 Hom.: 5230

Bravo AF: 0.348

Asia WGS AF: 0.180 AC: 629 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.5
DANN	Benign	0.35
PhyloP100		0.27

Splicing

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

Other links and lift over

dbSNP: rs1532926; hg19: chr16-8073918;