rs10512017

chr9-73269323-G-A

Variant summary

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

The XR_001746723.2(LOC101927281):n.67+9966G>A 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 0.0251 in 152,220 control chromosomes in the GnomAD database, including 85 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 0.025 (85 hom., cov: 32)
• Consequence: LOC101927281 XR_001746723.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.738

Genes affected

LOC101927281 (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 (AFR) allele frequency at 95% confidence interval = 0.0632 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101927281	XR_001746723.2	n.67+9966G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0252 AC: 3828 AN: 152102 Hom.: 87 Cov.: 32

Gnomad AFR AF: 0.0653

Gnomad AMI AF: 0.00877

Gnomad AMR AF: 0.0190

Gnomad ASJ AF: 0.0104

Gnomad EAS AF: 0.0272

Gnomad SAS AF: 0.0265

Gnomad FIN AF: 0.00226

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.00659

Gnomad OTH AF: 0.0191

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

GnomAD4 genome AF: 0.0251 AC: 3827 AN: 152220 Hom.: 85 Cov.: 32 AF XY: 0.0248 AC XY: 1848 AN XY: 74434

Gnomad4 AFR AF: 0.0652

Gnomad4 AMR AF: 0.0189

Gnomad4 ASJ AF: 0.0104

Gnomad4 EAS AF: 0.0264

Gnomad4 SAS AF: 0.0263

Gnomad4 FIN AF: 0.00226

Gnomad4 NFE AF: 0.00659

Gnomad4 OTH AF: 0.0189

Alfa AF: 0.0152 Hom.: 6

Bravo AF: 0.0277

Asia WGS AF: 0.0380 AC: 134 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.43
Dann	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10512017; hg19: chr9-75884239;