ENST00000778465.1:n.110-403G>C

Variant names:

• chr9-75455766-G-C
• rs2026406
• ENST00000778465.1:n.110-403G>C

Variant summary

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

The ENST00000778465.1(ENSG00000301354):​n.110-403G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.498 in 152,084 control chromosomes in the GnomAD database, including 19,437 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 0.50 (19437 hom., cov: 33)
• Consequence: ENSG00000301354 ENST00000778465.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.415
• Publications: 2 publications found

Genes affected

ENSG00000301354 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.543 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
ENSG00000301354	ENST00000778465.1	n.110-403G>C		intron_variant	Intron 1 of 1
ENSG00000301354	ENST00000778466.1	n.272-403G>C		intron_variant	Intron 2 of 2
ENSG00000301354	ENST00000778467.1	n.106-403G>C		intron_variant	Intron 1 of 1
ENSG00000301354	ENST00000778468.1	n.130-403G>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.498 AC: 75658 AN: 151966 Hom.: 19426 Cov.: 33

Gnomad AFR AF: 0.428

Gnomad AMI AF: 0.409

Gnomad AMR AF: 0.553

Gnomad ASJ AF: 0.434

Gnomad EAS AF: 0.313

Gnomad SAS AF: 0.314

Gnomad FIN AF: 0.657

Gnomad MID AF: 0.436

Gnomad NFE AF: 0.535

Gnomad OTH AF: 0.506

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

GnomAD4 genome AF: 0.498 AC: 75705 AN: 152084 Hom.: 19437 Cov.: 33 AF XY: 0.499 AC XY: 37119 AN XY: 74324

African (AFR) AF: 0.429 AC: 17793 AN: 41500

American (AMR) AF: 0.553 AC: 8439 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.434 AC: 1506 AN: 3472

East Asian (EAS) AF: 0.312 AC: 1610 AN: 5158

South Asian (SAS) AF: 0.312 AC: 1504 AN: 4814

European-Finnish (FIN) AF: 0.657 AC: 6936 AN: 10562

Middle Eastern (MID) AF: 0.428 AC: 125 AN: 292

European-Non Finnish (NFE) AF: 0.535 AC: 36359 AN: 67992

Other (OTH) AF: 0.502 AC: 1061 AN: 2112

Alfa AF: 0.522 Hom.: 2612

Bravo AF: 0.490

Asia WGS AF: 0.287 AC: 995 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	5.6
DANN	Benign	0.52
PhyloP100		0.41

Splicing

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

Other links and lift over

dbSNP: rs2026406; hg19: chr9-78070682;