rs10508275

Variant names:

• chr10-4073432-A-G
• rs10508275
• ENST00000455199.1:n.433-11765A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

Genes affected

ENSG00000236990 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LOC107984195	NR_176060.1	n.1190-5905A>G		intron_variant	Intron 4 of 9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000236990	ENST00000455199.1	n.433-11765A>G		intron_variant	Intron 1 of 3	2
ENSG00000236990	ENST00000846754.1	n.527-9844A>G		intron_variant	Intron 2 of 2
ENSG00000236990	ENST00000846755.1	n.143-9252A>G		intron_variant	Intron 1 of 3
ENSG00000236990	ENST00000846756.1	n.261-5905A>G		intron_variant	Intron 1 of 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

African (AFR) AF: 0.0182 AC: 757 AN: 41576

American (AMR) AF: 0.0871 AC: 1333 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.161 AC: 557 AN: 3470

East Asian (EAS) AF: 0.0667 AC: 346 AN: 5184

South Asian (SAS) AF: 0.0814 AC: 393 AN: 4828

European-Finnish (FIN) AF: 0.0545 AC: 578 AN: 10612

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.0896 AC: 6098 AN: 68028

Other (OTH) AF: 0.105 AC: 223 AN: 2116

Alfa AF: 0.0859 Hom.: 460

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
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs10508275; hg19: chr10-4115624;