ENST00000669683.1:n.856+6716T>A

Variant names:

• chr12-17487017-T-A
• rs10219673
• ENST00000669683.1:n.856+6716T>A

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000669683.1(ENSG00000256389):​n.856+6716T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.522 in 151,866 control chromosomes in the GnomAD database, including 20,753 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 0.52 (20753 hom., cov: 33)
• Consequence: ENSG00000256389 ENST00000669683.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.46
• Publications: 4 publications found

Genes affected

ENSG00000256389 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.19).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.598 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000256389	ENST00000669683.1	n.856+6716T>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.522 AC: 79190 AN: 151748 Hom.: 20733 Cov.: 33

Gnomad AFR AF: 0.515

Gnomad AMI AF: 0.520

Gnomad AMR AF: 0.547

Gnomad ASJ AF: 0.581

Gnomad EAS AF: 0.586

Gnomad SAS AF: 0.615

Gnomad FIN AF: 0.529

Gnomad MID AF: 0.566

Gnomad NFE AF: 0.504

Gnomad OTH AF: 0.519

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

GnomAD4 genome AF: 0.522 AC: 79262 AN: 151866 Hom.: 20753 Cov.: 33 AF XY: 0.525 AC XY: 38979 AN XY: 74226

African (AFR) AF: 0.515 AC: 21367 AN: 41458

American (AMR) AF: 0.547 AC: 8335 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.581 AC: 2010 AN: 3460

East Asian (EAS) AF: 0.586 AC: 3023 AN: 5160

South Asian (SAS) AF: 0.616 AC: 2975 AN: 4828

European-Finnish (FIN) AF: 0.529 AC: 5603 AN: 10592

Middle Eastern (MID) AF: 0.558 AC: 164 AN: 294

European-Non Finnish (NFE) AF: 0.504 AC: 34207 AN: 67820

Other (OTH) AF: 0.522 AC: 1104 AN: 2114

Alfa AF: 0.518 Hom.: 2535

Bravo AF: 0.524

Asia WGS AF: 0.612 AC: 2131 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.19
CADD	Benign	22
DANN	Benign	0.81
PhyloP100		2.5

Splicing

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

Other links and lift over

dbSNP: rs10219673; hg19: chr12-17639951;