ENST00000780276.1:n.299-534A>G

Variant names:

• chr14-68807188-T-C
• rs194749
• ENST00000780276.1:n.299-534A>G

Variant summary

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

The ENST00000780276.1(ENSG00000301622):​n.299-534A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.228 in 152,028 control chromosomes in the GnomAD database, including 4,065 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 0.23 (4065 hom., cov: 31)
• Consequence: ENSG00000301622 ENST00000780276.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.51
• Publications: 52 publications found

Genes affected

ENSG00000301622 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.279 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
ENSG00000301622	ENST00000780276.1	n.299-534A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.228 AC: 34637 AN: 151910 Hom.: 4064 Cov.: 31

Gnomad AFR AF: 0.204

Gnomad AMI AF: 0.284

Gnomad AMR AF: 0.233

Gnomad ASJ AF: 0.176

Gnomad EAS AF: 0.227

Gnomad SAS AF: 0.291

Gnomad FIN AF: 0.277

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.232

Gnomad OTH AF: 0.213

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

GnomAD4 genome AF: 0.228 AC: 34662 AN: 152028 Hom.: 4065 Cov.: 31 AF XY: 0.230 AC XY: 17126 AN XY: 74310

African (AFR) AF: 0.204 AC: 8457 AN: 41486

American (AMR) AF: 0.233 AC: 3553 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.176 AC: 608 AN: 3464

East Asian (EAS) AF: 0.227 AC: 1170 AN: 5162

South Asian (SAS) AF: 0.292 AC: 1407 AN: 4820

European-Finnish (FIN) AF: 0.277 AC: 2927 AN: 10576

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.232 AC: 15792 AN: 67944

Other (OTH) AF: 0.211 AC: 444 AN: 2102

Alfa AF: 0.224 Hom.: 15482

Bravo AF: 0.222

Asia WGS AF: 0.257 AC: 894 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.030
DANN	Benign	0.48
PhyloP100		-3.5

Splicing

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

Other links and lift over

dbSNP: rs194749; hg19: chr14-69273905;