ENST00000685798.1:n.453-13679G>A

Variant names:

• chr17-29348208-C-T
• rs11653144
• ENST00000685798.1:n.453-13679G>A

Variant summary

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

The ENST00000685798.1(ENSG00000264808):​n.453-13679G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.433 in 151,608 control chromosomes in the GnomAD database, including 15,607 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 0.43 (15607 hom., cov: 30)
• Consequence: ENSG00000264808 ENST00000685798.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.89
• Publications: 23 publications found

Genes affected

ENSG00000264808 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.864 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
ENSG00000264808	ENST00000685798.1	n.453-13679G>A		intron_variant	Intron 2 of 2
ENSG00000264808	ENST00000819810.1	n.493+21939G>A		intron_variant	Intron 2 of 2
ENSG00000264808	ENST00000819811.1	n.293+41729G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.433 AC: 65617 AN: 151490 Hom.: 15581 Cov.: 30

Gnomad AFR AF: 0.576

Gnomad AMI AF: 0.419

Gnomad AMR AF: 0.364

Gnomad ASJ AF: 0.322

Gnomad EAS AF: 0.885

Gnomad SAS AF: 0.507

Gnomad FIN AF: 0.380

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.338

Gnomad OTH AF: 0.384

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

GnomAD4 genome AF: 0.433 AC: 65678 AN: 151608 Hom.: 15607 Cov.: 30 AF XY: 0.441 AC XY: 32691 AN XY: 74090

African (AFR) AF: 0.576 AC: 23788 AN: 41280

American (AMR) AF: 0.365 AC: 5533 AN: 15174

Ashkenazi Jewish (ASJ) AF: 0.322 AC: 1116 AN: 3466

East Asian (EAS) AF: 0.885 AC: 4558 AN: 5150

South Asian (SAS) AF: 0.504 AC: 2427 AN: 4814

European-Finnish (FIN) AF: 0.380 AC: 4005 AN: 10530

Middle Eastern (MID) AF: 0.327 AC: 96 AN: 294

European-Non Finnish (NFE) AF: 0.338 AC: 22964 AN: 67892

Other (OTH) AF: 0.386 AC: 809 AN: 2096

Alfa AF: 0.373 Hom.: 41175

Bravo AF: 0.440

Asia WGS AF: 0.652 AC: 2271 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	8.1
DANN	Benign	0.74
PhyloP100		1.9

Splicing

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

Other links and lift over

dbSNP: rs11653144; hg19: chr17-27675226;