ENST00000670669.1:n.130+4440G>A

Variant names:

• chr8-25597766-G-A
• rs7812975
• ENST00000670669.1:n.130+4440G>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000670669.1(ENSG00000253100):​n.130+4440G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.606 in 152,030 control chromosomes in the GnomAD database, including 29,717 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 0.61 (29717 hom., cov: 32)
• Consequence: ENSG00000253100 ENST00000670669.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.813

Genes affected

ENSG00000253100 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.722 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
ENSG00000253100	ENST00000670669.1	n.130+4440G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.606 AC: 92110 AN: 151912 Hom.: 29712 Cov.: 32

Gnomad AFR AF: 0.362

Gnomad AMI AF: 0.745

Gnomad AMR AF: 0.733

Gnomad ASJ AF: 0.737

Gnomad EAS AF: 0.722

Gnomad SAS AF: 0.688

Gnomad FIN AF: 0.664

Gnomad MID AF: 0.617

Gnomad NFE AF: 0.694

Gnomad OTH AF: 0.619

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

GnomAD4 genome AF: 0.606 AC: 92123 AN: 152030 Hom.: 29717 Cov.: 32 AF XY: 0.608 AC XY: 45139 AN XY: 74282

Gnomad4 AFR AF: 0.361

Gnomad4 AMR AF: 0.733

Gnomad4 ASJ AF: 0.737

Gnomad4 EAS AF: 0.721

Gnomad4 SAS AF: 0.689

Gnomad4 FIN AF: 0.664

Gnomad4 NFE AF: 0.694

Gnomad4 OTH AF: 0.625

Alfa AF: 0.677 Hom.: 17704

Bravo AF: 0.603

Asia WGS AF: 0.736 AC: 2558 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.24
DANN	Benign	0.17

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7812975; hg19: chr8-25455282;