rs10512019

chr9-73336360-T-C

Variant summary

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

The XR_001746723.2(LOC101927281):n.68-22448T>C 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 0.027 in 152,248 control chromosomes in the GnomAD database, including 87 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 0.027 (87 hom., cov: 32)
• Consequence: LOC101927281 XR_001746723.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.230

Genes affected

LOC101927281 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0633 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101927281	XR_001746723.2	n.68-22448T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0270 AC: 4111 AN: 152130 Hom.: 89 Cov.: 32

Gnomad AFR AF: 0.0654

Gnomad AMI AF: 0.00877

Gnomad AMR AF: 0.0192

Gnomad ASJ AF: 0.00893

Gnomad EAS AF: 0.0264

Gnomad SAS AF: 0.0313

Gnomad FIN AF: 0.00235

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0102

Gnomad OTH AF: 0.0235

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

GnomAD4 genome AF: 0.0270 AC: 4110 AN: 152248 Hom.: 87 Cov.: 32 AF XY: 0.0266 AC XY: 1978 AN XY: 74452

Gnomad4 AFR AF: 0.0654

Gnomad4 AMR AF: 0.0192

Gnomad4 ASJ AF: 0.00893

Gnomad4 EAS AF: 0.0255

Gnomad4 SAS AF: 0.0311

Gnomad4 FIN AF: 0.00235

Gnomad4 NFE AF: 0.0102

Gnomad4 OTH AF: 0.0232

Alfa AF: 0.0184 Hom.: 8

Bravo AF: 0.0288

Asia WGS AF: 0.0440 AC: 153 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	1.3
Dann	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10512019; hg19: chr9-75951276;