9-21954954-A-G

Variant names:

• chr9-21954954-A-G
• rs10757261
• ENST00000404796.3:n.461-74479A>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000404796.3(ENSG00000264545):​n.461-74479A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.547 in 152,026 control chromosomes in the GnomAD database, including 24,091 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 0.55 (24091 hom., cov: 31)
• Consequence: ENSG00000264545 ENST00000404796.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.619

Genes affected

ENSG00000264545 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.663 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
ENSG00000264545	ENST00000404796.3	n.461-74479A>G		intron_variant	Intron 4 of 4	5

Frequencies

GnomAD3 genomes AF: 0.547 AC: 83158 AN: 151906 Hom.: 24100 Cov.: 31

Gnomad AFR AF: 0.351

Gnomad AMI AF: 0.533

Gnomad AMR AF: 0.496

Gnomad ASJ AF: 0.604

Gnomad EAS AF: 0.663

Gnomad SAS AF: 0.683

Gnomad FIN AF: 0.669

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.639

Gnomad OTH AF: 0.542

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

GnomAD4 genome AF: 0.547 AC: 83160 AN: 152026 Hom.: 24091 Cov.: 31 AF XY: 0.550 AC XY: 40875 AN XY: 74304

Gnomad4 AFR AF: 0.351

Gnomad4 AMR AF: 0.496

Gnomad4 ASJ AF: 0.604

Gnomad4 EAS AF: 0.663

Gnomad4 SAS AF: 0.682

Gnomad4 FIN AF: 0.669

Gnomad4 NFE AF: 0.639

Gnomad4 OTH AF: 0.539

Alfa AF: 0.570 Hom.: 5721

Bravo AF: 0.521

Asia WGS AF: 0.641 AC: 2232 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.9
DANN	Benign	0.66

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs10757261; hg19: chr9-21954953;