ENST00000667782.1:n.574+25803A>G

Variant names:

• chr2-77715718-T-C
• rs11126630
• ENST00000667782.1:n.574+25803A>G

Variant summary

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

The ENST00000667782.1(ENSG00000227088):​n.574+25803A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.421 in 151,744 control chromosomes in the GnomAD database, including 14,761 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 0.42 (14761 hom., cov: 32)
• Consequence: ENSG00000227088 ENST00000667782.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0390
• Publications: 11 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=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.554 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
ENSG00000227088	ENST00000667782.1	n.574+25803A>G		intron_variant	Intron 6 of 6
ENSG00000227088	ENST00000828171.1	n.281+25803A>G		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.421 AC: 63866 AN: 151626 Hom.: 14763 Cov.: 32

Gnomad AFR AF: 0.228

Gnomad AMI AF: 0.498

Gnomad AMR AF: 0.414

Gnomad ASJ AF: 0.586

Gnomad EAS AF: 0.473

Gnomad SAS AF: 0.572

Gnomad FIN AF: 0.454

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.510

Gnomad OTH AF: 0.447

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

GnomAD4 genome AF: 0.421 AC: 63882 AN: 151744 Hom.: 14761 Cov.: 32 AF XY: 0.419 AC XY: 31027 AN XY: 74132

African (AFR) AF: 0.228 AC: 9448 AN: 41456

American (AMR) AF: 0.414 AC: 6281 AN: 15186

Ashkenazi Jewish (ASJ) AF: 0.586 AC: 2033 AN: 3468

East Asian (EAS) AF: 0.473 AC: 2429 AN: 5134

South Asian (SAS) AF: 0.571 AC: 2753 AN: 4818

European-Finnish (FIN) AF: 0.454 AC: 4779 AN: 10530

Middle Eastern (MID) AF: 0.531 AC: 155 AN: 292

European-Non Finnish (NFE) AF: 0.510 AC: 34614 AN: 67844

Other (OTH) AF: 0.445 AC: 938 AN: 2108

Alfa AF: 0.348 Hom.: 1364

Bravo AF: 0.406

Asia WGS AF: 0.555 AC: 1902 AN: 3432

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.5
DANN	Benign	0.80
PhyloP100		0.039

Splicing

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

Other links and lift over

dbSNP: rs11126630; hg19: chr2-77942844;