rs10512152

Positions:

• chr9-84612894-A-G

Variant summary

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

The ENST00000650453.1(ENSG00000285987):​n.1341+897A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0262 in 152,264 control chromosomes in the GnomAD database, including 78 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 0.026 (78 hom., cov: 33)
• Consequence: ENST00000650453.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.07

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0514 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC102724036	XR_007061623.1	n.7136+897A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000650453.1	n.1341+897A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0262 AC: 3987 AN: 152146 Hom.: 78 Cov.: 33

Gnomad AFR AF: 0.00731

Gnomad AMI AF: 0.122

Gnomad AMR AF: 0.0546

Gnomad ASJ AF: 0.0135

Gnomad EAS AF: 0.0494

Gnomad SAS AF: 0.0172

Gnomad FIN AF: 0.0294

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.0293

Gnomad OTH AF: 0.0234

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

GnomAD4 genome AF: 0.0262 AC: 3987 AN: 152264 Hom.: 78 Cov.: 33 AF XY: 0.0266 AC XY: 1982 AN XY: 74452

Gnomad4 AFR AF: 0.00729

Gnomad4 AMR AF: 0.0545

Gnomad4 ASJ AF: 0.0135

Gnomad4 EAS AF: 0.0494

Gnomad4 SAS AF: 0.0176

Gnomad4 FIN AF: 0.0294

Gnomad4 NFE AF: 0.0293

Gnomad4 OTH AF: 0.0232

Alfa AF: 0.0292 Hom.: 10

Bravo AF: 0.0283

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.050
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10512152; hg19: chr9-87227809;