9-134525462-G-T

Variant summary

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

The XR_930417.3(LOC100506532):n.352-19458G>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 0.418 in 152,108 control chromosomes in the GnomAD database, including 13,520 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 0.42 (13520 hom., cov: 34)
• Consequence: LOC100506532 XR_930417.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.267

Genes affected

LOC100506532 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.467 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC100506532	XR_930417.3	n.352-19458G>T		intron_variant, non_coding_transcript_variant
LOC100506532	XR_109854.6	n.410G>T		non_coding_transcript_exon_variant	1/2
LOC100506532	XR_930416.3	n.181-19458G>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.418 AC: 63563 AN: 151990 Hom.: 13529 Cov.: 34

Gnomad AFR AF: 0.362

Gnomad AMI AF: 0.492

Gnomad AMR AF: 0.476

Gnomad ASJ AF: 0.520

Gnomad EAS AF: 0.436

Gnomad SAS AF: 0.361

Gnomad FIN AF: 0.383

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.441

Gnomad OTH AF: 0.431

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

GnomAD4 genome AF: 0.418 AC: 63588 AN: 152108 Hom.: 13520 Cov.: 34 AF XY: 0.417 AC XY: 30985 AN XY: 74338

Gnomad4 AFR AF: 0.362

Gnomad4 AMR AF: 0.476

Gnomad4 ASJ AF: 0.520

Gnomad4 EAS AF: 0.436

Gnomad4 SAS AF: 0.361

Gnomad4 FIN AF: 0.383

Gnomad4 NFE AF: 0.441

Gnomad4 OTH AF: 0.428

Alfa AF: 0.448 Hom.: 14422

Bravo AF: 0.428

Asia WGS AF: 0.409 AC: 1423 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	3.7
Dann	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10776839; hg19: chr9-137417308;