ENST00000667782.1:n.83-94391T>C

Variant names:

• chr2-78034277-A-G
• rs2204599
• ENST00000667782.1:n.83-94391T>C

Variant summary

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

The ENST00000667782.1(ENSG00000227088):​n.83-94391T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.86 in 152,070 control chromosomes in the GnomAD database, including 56,465 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 0.86 (56465 hom., cov: 33)
• Consequence: ENSG00000227088 ENST00000667782.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.90
• Publications: 1 publications found

Genes affected

ENSG00000227088 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.918 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101927967	NR_110288.1	n.345-159215T>C		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000227088	ENST00000667782.1	n.83-94391T>C		intron_variant	Intron 1 of 6

Frequencies

GnomAD3 genomes AF: 0.860 AC: 130713 AN: 151942 Hom.: 56410 Cov.: 33

Gnomad AFR AF: 0.925

Gnomad AMI AF: 0.829

Gnomad AMR AF: 0.846

Gnomad ASJ AF: 0.835

Gnomad EAS AF: 0.903

Gnomad SAS AF: 0.908

Gnomad FIN AF: 0.869

Gnomad MID AF: 0.864

Gnomad NFE AF: 0.817

Gnomad OTH AF: 0.863

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

GnomAD4 genome AF: 0.860 AC: 130832 AN: 152070 Hom.: 56465 Cov.: 33 AF XY: 0.865 AC XY: 64299 AN XY: 74354

African (AFR) AF: 0.926 AC: 38428 AN: 41520

American (AMR) AF: 0.846 AC: 12915 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.835 AC: 2896 AN: 3470

East Asian (EAS) AF: 0.903 AC: 4663 AN: 5166

South Asian (SAS) AF: 0.908 AC: 4373 AN: 4814

European-Finnish (FIN) AF: 0.869 AC: 9206 AN: 10598

Middle Eastern (MID) AF: 0.867 AC: 241 AN: 278

European-Non Finnish (NFE) AF: 0.817 AC: 55538 AN: 67950

Other (OTH) AF: 0.864 AC: 1819 AN: 2106

Alfa AF: 0.830 Hom.: 10504

Bravo AF: 0.861

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.18
DANN	Benign	0.71
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs2204599; hg19: chr2-78261403;