ENST00000421889.1:n.109-1079A>G

Variant names:

• chr10-79935452-A-G
• rs1923537
• ENST00000421889.1:n.109-1079A>G

Variant summary

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

The ENST00000421889.1(ENSG00000283913):​n.109-1079A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.372 in 151,884 control chromosomes in the GnomAD database, including 10,854 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 0.37 (10854 hom., cov: 31)
• Consequence: ENSG00000283913 ENST00000421889.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.36

Genes affected

ENSG00000283913 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.468 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
ENSG00000283913	ENST00000421889.1	n.109-1079A>G		intron_variant	Intron 1 of 3	3
ENSG00000283913	ENST00000453174.7	n.836-1079A>G		intron_variant	Intron 6 of 7	2

Frequencies

GnomAD3 genomes AF: 0.373 AC: 56534 AN: 151766 Hom.: 10858 Cov.: 31

Gnomad AFR AF: 0.367

Gnomad AMI AF: 0.498

Gnomad AMR AF: 0.273

Gnomad ASJ AF: 0.270

Gnomad EAS AF: 0.484

Gnomad SAS AF: 0.388

Gnomad FIN AF: 0.464

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.379

Gnomad OTH AF: 0.347

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

GnomAD4 genome AF: 0.372 AC: 56560 AN: 151884 Hom.: 10854 Cov.: 31 AF XY: 0.375 AC XY: 27804 AN XY: 74212

Gnomad4 AFR AF: 0.366

Gnomad4 AMR AF: 0.274

Gnomad4 ASJ AF: 0.270

Gnomad4 EAS AF: 0.484

Gnomad4 SAS AF: 0.388

Gnomad4 FIN AF: 0.464

Gnomad4 NFE AF: 0.379

Gnomad4 OTH AF: 0.345

Alfa AF: 0.379 Hom.: 1644

Bravo AF: 0.358

Asia WGS AF: 0.438 AC: 1523 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.41
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1923537; hg19: chr10-81695208;