10-23569282-G-A

Variant names:

• chr10-23569282-G-A
• rs16923476
• ENST00000829265.1:n.271-411G>A

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000829265.1(ENSG00000307832):​n.271-411G>A variant causes a intron change. The variant allele was found at a frequency of 0.0969 in 151,936 control chromosomes in the GnomAD database, including 1,507 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 0.097 (1507 hom., cov: 31)
• Consequence: ENSG00000307832 ENST00000829265.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.78
• Publications: 8 publications found

Genes affected

ENSG00000307832 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.45).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.253 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105376454	XR_930753.3	n.1151+480G>A		intron_variant	Intron 5 of 10
LOC105376454	XR_930754.3	n.1151+480G>A		intron_variant	Intron 5 of 8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000307832	ENST00000829265.1	n.271-411G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.0967 AC: 14686 AN: 151818 Hom.: 1497 Cov.: 31

Gnomad AFR AF: 0.257

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0949

Gnomad ASJ AF: 0.0276

Gnomad EAS AF: 0.00270

Gnomad SAS AF: 0.102

Gnomad FIN AF: 0.00890

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0263

Gnomad OTH AF: 0.0778

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

GnomAD4 genome AF: 0.0969 AC: 14724 AN: 151936 Hom.: 1507 Cov.: 31 AF XY: 0.0956 AC XY: 7101 AN XY: 74248

African (AFR) AF: 0.257 AC: 10609 AN: 41328

American (AMR) AF: 0.0950 AC: 1450 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.0276 AC: 96 AN: 3472

East Asian (EAS) AF: 0.00270 AC: 14 AN: 5176

South Asian (SAS) AF: 0.102 AC: 494 AN: 4822

European-Finnish (FIN) AF: 0.00890 AC: 94 AN: 10562

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0263 AC: 1791 AN: 68004

Other (OTH) AF: 0.0765 AC: 161 AN: 2104

Alfa AF: 0.102 Hom.: 879

Bravo AF: 0.110

Asia WGS AF: 0.0830 AC: 289 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.45
CADD	Benign	15
DANN	Benign	0.63
PhyloP100		3.8

Splicing

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

Other links and lift over

dbSNP: rs16923476; hg19: chr10-23858211;