ENST00000716817.1:n.182+791T>A

Variant names:

• chr14-48319874-A-T
• rs1769490
• ENST00000716817.1:n.182+791T>A

Variant summary

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

The ENST00000716817.1(ENSG00000258751):​n.182+791T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.597 in 150,892 control chromosomes in the GnomAD database, including 27,544 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 0.60 (27544 hom., cov: 27)
• Consequence: ENSG00000258751 ENST00000716817.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.241
• Publications: 2 publications found

Genes affected

ENSG00000258751 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.66 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
ENSG00000258751	ENST00000716817.1	n.182+791T>A		intron_variant	Intron 3 of 3
ENSG00000258751	ENST00000716818.1	n.180+791T>A		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.598 AC: 90110 AN: 150780 Hom.: 27547 Cov.: 27

Gnomad AFR AF: 0.512

Gnomad AMI AF: 0.556

Gnomad AMR AF: 0.546

Gnomad ASJ AF: 0.642

Gnomad EAS AF: 0.313

Gnomad SAS AF: 0.547

Gnomad FIN AF: 0.713

Gnomad MID AF: 0.583

Gnomad NFE AF: 0.665

Gnomad OTH AF: 0.622

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

GnomAD4 genome AF: 0.597 AC: 90132 AN: 150892 Hom.: 27544 Cov.: 27 AF XY: 0.597 AC XY: 43919 AN XY: 73624

African (AFR) AF: 0.512 AC: 21035 AN: 41108

American (AMR) AF: 0.546 AC: 8233 AN: 15092

Ashkenazi Jewish (ASJ) AF: 0.642 AC: 2225 AN: 3466

East Asian (EAS) AF: 0.313 AC: 1578 AN: 5046

South Asian (SAS) AF: 0.547 AC: 2611 AN: 4770

European-Finnish (FIN) AF: 0.713 AC: 7378 AN: 10346

Middle Eastern (MID) AF: 0.590 AC: 170 AN: 288

European-Non Finnish (NFE) AF: 0.665 AC: 45106 AN: 67788

Other (OTH) AF: 0.620 AC: 1302 AN: 2100

Alfa AF: 0.533 Hom.: 1697

Bravo AF: 0.577

Asia WGS AF: 0.445 AC: 1550 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.3
DANN	Benign	0.70
PhyloP100		0.24

Splicing

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

Other links and lift over

dbSNP: rs1769490; hg19: chr14-48789077;