9-134936804-T-G

Variant summary

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

The XR_007061846.1(LOC124902302):n.4754A>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.47 in 151,978 control chromosomes in the GnomAD database, including 17,009 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 0.47 (17009 hom., cov: 32)
• Consequence: LOC124902302 XR_007061846.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.56

Genes affected

LOC124902302 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.554 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124902302	XR_007061846.1	n.4754A>C		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000664778.1	n.50+231T>G		intron_variant, non_coding_transcript_variant
	ENST00000654026.1	n.206T>G		non_coding_transcript_exon_variant	1/4
	ENST00000663742.1	n.180T>G		non_coding_transcript_exon_variant	1/3

Frequencies

GnomAD3 genomes AF: 0.470 AC: 71406 AN: 151856 Hom.: 17011 Cov.: 32

Gnomad AFR AF: 0.422

Gnomad AMI AF: 0.590

Gnomad AMR AF: 0.376

Gnomad ASJ AF: 0.517

Gnomad EAS AF: 0.572

Gnomad SAS AF: 0.497

Gnomad FIN AF: 0.442

Gnomad MID AF: 0.564

Gnomad NFE AF: 0.511

Gnomad OTH AF: 0.475

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

GnomAD4 genome AF: 0.470 AC: 71420 AN: 151978 Hom.: 17009 Cov.: 32 AF XY: 0.466 AC XY: 34592 AN XY: 74288

Gnomad4 AFR AF: 0.421

Gnomad4 AMR AF: 0.375

Gnomad4 ASJ AF: 0.517

Gnomad4 EAS AF: 0.571

Gnomad4 SAS AF: 0.499

Gnomad4 FIN AF: 0.442

Gnomad4 NFE AF: 0.511

Gnomad4 OTH AF: 0.473

Alfa AF: 0.419 Hom.: 3089

Bravo AF: 0.459

Asia WGS AF: 0.479 AC: 1667 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	0.015
Dann	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1105176; hg19: chr9-137828650;