rs10825992

Variant names:

• chr10-57188447-T-G
• rs10825992
• ENST00000690550.2:n.146+34165A>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000690550.2(ENSG00000289158):​n.146+34165A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.437 in 151,340 control chromosomes in the GnomAD database, including 17,168 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 0.44 (17168 hom., cov: 31)
• Consequence: ENSG00000289158 ENST00000690550.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.137
• Publications: 3 publications found

Genes affected

ENSG00000289158 (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 (AFR) allele frequency at 95% confidence interval = 0.725 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
ENSG00000289158	ENST00000690550.2	n.146+34165A>C		intron_variant	Intron 1 of 2
ENSG00000289158	ENST00000752897.1	n.151+34165A>C		intron_variant	Intron 1 of 3
ENSG00000289158	ENST00000752899.1	n.66+34165A>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.437 AC: 66072 AN: 151220 Hom.: 17147 Cov.: 31

Gnomad AFR AF: 0.732

Gnomad AMI AF: 0.402

Gnomad AMR AF: 0.340

Gnomad ASJ AF: 0.227

Gnomad EAS AF: 0.129

Gnomad SAS AF: 0.353

Gnomad FIN AF: 0.301

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.341

Gnomad OTH AF: 0.421

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

GnomAD4 genome AF: 0.437 AC: 66142 AN: 151340 Hom.: 17168 Cov.: 31 AF XY: 0.431 AC XY: 31862 AN XY: 73964

African (AFR) AF: 0.731 AC: 30238 AN: 41340

American (AMR) AF: 0.340 AC: 5157 AN: 15164

Ashkenazi Jewish (ASJ) AF: 0.227 AC: 785 AN: 3456

East Asian (EAS) AF: 0.129 AC: 666 AN: 5164

South Asian (SAS) AF: 0.351 AC: 1692 AN: 4818

European-Finnish (FIN) AF: 0.301 AC: 3174 AN: 10544

Middle Eastern (MID) AF: 0.449 AC: 132 AN: 294

European-Non Finnish (NFE) AF: 0.341 AC: 23054 AN: 67548

Other (OTH) AF: 0.418 AC: 878 AN: 2102

Alfa AF: 0.365 Hom.: 6352

Bravo AF: 0.456

Asia WGS AF: 0.279 AC: 965 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.0
DANN	Benign	0.50
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs10825992; hg19: chr10-58948207;