9-82521969-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 XR_001746782.2(LOC107987087):​n.247+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: LOC107987087 XR_001746782.2 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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000589973.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000290551	ENST00000589973.3	TSL:5	n.501+25111A>G		intron	N/A
	ENSG00000290551	ENST00000590298.5	TSL:5	n.440-42060A>G		intron	N/A
	ENSG00000290551	ENST00000590791.5	TSL:5	n.526-2550A>G		intron	N/A

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 v4.9

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;