rs10413089

Variant names:

• chr19-44952331-T-C
• rs10413089
• ENST00000591646.1:n.114-1305A>G

Variant summary

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

The ENST00000591646.1(ENSG00000267114):​n.114-1305A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.21 in 152,190 control chromosomes in the GnomAD database, including 3,694 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 0.21 (3694 hom., cov: 32)
• Consequence: ENSG00000267114 ENST00000591646.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0870

Genes affected

ENSG00000267114 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.321 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
ENSG00000267114	ENST00000591646.1	n.114-1305A>G		intron_variant	Intron 1 of 2	3

Frequencies

GnomAD3 genomes AF: 0.210 AC: 32006 AN: 152072 Hom.: 3689 Cov.: 32

Gnomad AFR AF: 0.281

Gnomad AMI AF: 0.279

Gnomad AMR AF: 0.205

Gnomad ASJ AF: 0.157

Gnomad EAS AF: 0.0866

Gnomad SAS AF: 0.336

Gnomad FIN AF: 0.147

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.182

Gnomad OTH AF: 0.182

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

GnomAD4 genome AF: 0.210 AC: 32031 AN: 152190 Hom.: 3694 Cov.: 32 AF XY: 0.210 AC XY: 15596 AN XY: 74402

Gnomad4 AFR AF: 0.281

Gnomad4 AMR AF: 0.205

Gnomad4 ASJ AF: 0.157

Gnomad4 EAS AF: 0.0861

Gnomad4 SAS AF: 0.335

Gnomad4 FIN AF: 0.147

Gnomad4 NFE AF: 0.182

Gnomad4 OTH AF: 0.180

Alfa AF: 0.186 Hom.: 5771

Bravo AF: 0.215

Asia WGS AF: 0.206 AC: 716 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.1
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10413089; hg19: chr19-45455588;