ENST00000717079.1:n.400+6427T>G

Variant names:

• chr1-230818237-A-C
• rs12062054
• ENST00000717079.1:n.400+6427T>G

Variant summary

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

The ENST00000717079.1(ENSG00000225656):​n.400+6427T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.239 in 151,840 control chromosomes in the GnomAD database, including 5,982 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 0.24 (5982 hom., cov: 31)
• Consequence: ENSG00000225656 ENST00000717079.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0560
• Publications: 2 publications found

Genes affected

ENSG00000225656 (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 = 0.466 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
ENSG00000225656	ENST00000717079.1	n.400+6427T>G		intron_variant	Intron 1 of 1
ENSG00000225656	ENST00000789895.1	n.121+6427T>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.239 AC: 36218 AN: 151722 Hom.: 5962 Cov.: 31

Gnomad AFR AF: 0.471

Gnomad AMI AF: 0.175

Gnomad AMR AF: 0.206

Gnomad ASJ AF: 0.209

Gnomad EAS AF: 0.139

Gnomad SAS AF: 0.273

Gnomad FIN AF: 0.133

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.129

Gnomad OTH AF: 0.213

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

GnomAD4 genome AF: 0.239 AC: 36296 AN: 151840 Hom.: 5982 Cov.: 31 AF XY: 0.240 AC XY: 17833 AN XY: 74192

African (AFR) AF: 0.471 AC: 19498 AN: 41368

American (AMR) AF: 0.206 AC: 3134 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.209 AC: 725 AN: 3466

East Asian (EAS) AF: 0.140 AC: 721 AN: 5158

South Asian (SAS) AF: 0.273 AC: 1311 AN: 4806

European-Finnish (FIN) AF: 0.133 AC: 1398 AN: 10538

Middle Eastern (MID) AF: 0.337 AC: 99 AN: 294

European-Non Finnish (NFE) AF: 0.129 AC: 8798 AN: 67946

Other (OTH) AF: 0.215 AC: 452 AN: 2106

Alfa AF: 0.168 Hom.: 4547

Bravo AF: 0.251

Asia WGS AF: 0.251 AC: 874 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	5.8
DANN	Benign	0.48
PhyloP100		0.056

Splicing

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

Other links and lift over

dbSNP: rs12062054; hg19: chr1-230953983;