chr9-82521969-A-G

Variant names:

• chr9-82521969-A-G
• rs10121807
• ENST00000589973.3:n.501+25111A>G

Variant summary

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

The ENST00000589973.3(ENSG00000290551):​n.501+25111A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.132 in 152,100 control chromosomes in the GnomAD database, including 1,897 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 0.13 (1897 hom., cov: 32)
• Consequence: ENSG00000290551 ENST00000589973.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.05
• Publications: 0 publications found

Genes affected

ENSG00000290551 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.267 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107987087	XR_001746782.2	n.247+25111A>G		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000290551	ENST00000589973.3	n.501+25111A>G		intron_variant	Intron 5 of 5	5
ENSG00000290551	ENST00000590298.5	n.440-42060A>G		intron_variant	Intron 6 of 6	5
ENSG00000290551	ENST00000590791.5	n.526-2550A>G		intron_variant	Intron 5 of 5	5

Frequencies

GnomAD3 genomes AF: 0.132 AC: 20078 AN: 151980 Hom.: 1883 Cov.: 32

Gnomad AFR AF: 0.271

Gnomad AMI AF: 0.0285

Gnomad AMR AF: 0.0725

Gnomad ASJ AF: 0.0637

Gnomad EAS AF: 0.0574

Gnomad SAS AF: 0.0498

Gnomad FIN AF: 0.0612

Gnomad MID AF: 0.0828

Gnomad NFE AF: 0.0895

Gnomad OTH AF: 0.109

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

GnomAD4 genome AF: 0.132 AC: 20136 AN: 152100 Hom.: 1897 Cov.: 32 AF XY: 0.127 AC XY: 9427 AN XY: 74350

African (AFR) AF: 0.271 AC: 11261 AN: 41494

American (AMR) AF: 0.0724 AC: 1106 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.0637 AC: 221 AN: 3470

East Asian (EAS) AF: 0.0573 AC: 296 AN: 5164

South Asian (SAS) AF: 0.0494 AC: 238 AN: 4820

European-Finnish (FIN) AF: 0.0612 AC: 648 AN: 10596

Middle Eastern (MID) AF: 0.0822 AC: 24 AN: 292

European-Non Finnish (NFE) AF: 0.0895 AC: 6083 AN: 67974

Other (OTH) AF: 0.110 AC: 233 AN: 2112

Alfa AF: 0.105 Hom.: 1786

Bravo AF: 0.142

Asia WGS AF: 0.0790 AC: 275 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.0040
DANN	Benign	0.38
PhyloP100		-3.0

Splicing

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

Other links and lift over

dbSNP: rs10121807; hg19: chr9-85136884;