rs10508275

Positions:

• chr10-4073432-A-G

Variant summary

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

The ENST00000455199.1(ENSG00000236990):​n.433-11765A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0687 in 152,314 control chromosomes in the GnomAD database, including 465 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 0.069 (465 hom., cov: 33)
• Consequence: ENSG00000236990 ENST00000455199.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.214

Genes affected

ENSG00000236990 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0878 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107984195	NR_176060.1	n.1190-5905A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000236990	ENST00000455199.1	n.433-11765A>G		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.0687 AC: 10462 AN: 152196 Hom.: 465 Cov.: 33

Gnomad AFR AF: 0.0182

Gnomad AMI AF: 0.130

Gnomad AMR AF: 0.0871

Gnomad ASJ AF: 0.161

Gnomad EAS AF: 0.0668

Gnomad SAS AF: 0.0815

Gnomad FIN AF: 0.0545

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.0896

Gnomad OTH AF: 0.107

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

GnomAD4 genome AF: 0.0687 AC: 10457 AN: 152314 Hom.: 465 Cov.: 33 AF XY: 0.0680 AC XY: 5066 AN XY: 74474

Gnomad4 AFR AF: 0.0182

Gnomad4 AMR AF: 0.0871

Gnomad4 ASJ AF: 0.161

Gnomad4 EAS AF: 0.0667

Gnomad4 SAS AF: 0.0814

Gnomad4 FIN AF: 0.0545

Gnomad4 NFE AF: 0.0896

Gnomad4 OTH AF: 0.105

Alfa AF: 0.0850 Hom.: 319

Bravo AF: 0.0709

Asia WGS AF: 0.0720 AC: 252 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.85
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10508275; hg19: chr10-4115624;