rs10521453

chr9-73422600-G-A

Variant summary

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

The XR_001746729.1(LOC105376083):n.994+499C>T 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 0.0272 in 151,856 control chromosomes in the GnomAD database, including 91 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 (91 hom., cov: 32)
• Consequence: LOC105376083 XR_001746729.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.796

Genes affected

LOC105376083 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.064 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105376083	XR_001746729.1	n.994+499C>T		intron_variant, non_coding_transcript_variant
LOC105376084	XR_007061581.1	n.90-3002G>A		intron_variant, non_coding_transcript_variant
LOC105376084	XR_929939.1	n.90-3002G>A		intron_variant, non_coding_transcript_variant
LOC105376084	XR_929941.2	n.90-3002G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0272 AC: 4126 AN: 151738 Hom.: 93 Cov.: 32

Gnomad AFR AF: 0.0661

Gnomad AMI AF: 0.00877

Gnomad AMR AF: 0.0194

Gnomad ASJ AF: 0.00894

Gnomad EAS AF: 0.0258

Gnomad SAS AF: 0.0311

Gnomad FIN AF: 0.00236

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0102

Gnomad OTH AF: 0.0225

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

GnomAD4 genome AF: 0.0272 AC: 4125 AN: 151856 Hom.: 91 Cov.: 32 AF XY: 0.0267 AC XY: 1979 AN XY: 74204

Gnomad4 AFR AF: 0.0661

Gnomad4 AMR AF: 0.0194

Gnomad4 ASJ AF: 0.00894

Gnomad4 EAS AF: 0.0249

Gnomad4 SAS AF: 0.0309

Gnomad4 FIN AF: 0.00236

Gnomad4 NFE AF: 0.0102

Gnomad4 OTH AF: 0.0223

Alfa AF: 0.0177 Hom.: 8

Bravo AF: 0.0290

Asia WGS AF: 0.0430 AC: 151 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.57
Dann	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10521453; hg19: chr9-76037516;