ENST00000554307.1:n.366+28204A>G

Variant names:

• chr14-79944098-T-C
• rs8010717
• ENST00000554307.1:n.366+28204A>G

Variant summary

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

The ENST00000554307.1(ENSG00000258416):​n.366+28204A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.285 in 152,104 control chromosomes in the GnomAD database, including 6,229 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 0.29 (6229 hom., cov: 33)
• Consequence: ENSG00000258416 ENST00000554307.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.21
• Publications: 4 publications found

Genes affected

ENSG00000258416 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.286 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107984630	XR_001751015.3	n.86+6T>C		splice_region_variant, intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000258416	ENST00000554307.1	n.366+28204A>G		intron_variant	Intron 2 of 2	3
ENSG00000310098	ENST00000847126.1	n.351+6T>C		splice_region_variant, intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.285 AC: 43357 AN: 151986 Hom.: 6216 Cov.: 33

Gnomad AFR AF: 0.260

Gnomad AMI AF: 0.216

Gnomad AMR AF: 0.288

Gnomad ASJ AF: 0.226

Gnomad EAS AF: 0.275

Gnomad SAS AF: 0.286

Gnomad FIN AF: 0.391

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.290

Gnomad OTH AF: 0.254

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

GnomAD4 genome AF: 0.285 AC: 43412 AN: 152104 Hom.: 6229 Cov.: 33 AF XY: 0.289 AC XY: 21470 AN XY: 74328

African (AFR) AF: 0.260 AC: 10798 AN: 41502

American (AMR) AF: 0.288 AC: 4408 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.226 AC: 785 AN: 3472

East Asian (EAS) AF: 0.275 AC: 1417 AN: 5150

South Asian (SAS) AF: 0.287 AC: 1385 AN: 4826

European-Finnish (FIN) AF: 0.391 AC: 4130 AN: 10562

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.290 AC: 19702 AN: 67992

Other (OTH) AF: 0.255 AC: 539 AN: 2112

Alfa AF: 0.278 Hom.: 2057

Bravo AF: 0.279

Asia WGS AF: 0.271 AC: 941 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.83
DANN	Benign	0.37
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs8010717; hg19: chr14-80410441;