3-117152001-T-C

Variant summary

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

The XR_007096015.1(LOC124909415):n.29329+97015A>G 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 0.884 in 152,166 control chromosomes in the GnomAD database, including 59,586 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 0.88 (59586 hom., cov: 31)
• Consequence: LOC124909415 XR_007096015.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.638

Genes affected

LOC124909415 (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 = 0.97 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124909415	XR_007096015.1	n.29329+97015A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.884 AC: 134417 AN: 152048 Hom.: 59523 Cov.: 31

Gnomad AFR AF: 0.915

Gnomad AMI AF: 0.840

Gnomad AMR AF: 0.908

Gnomad ASJ AF: 0.880

Gnomad EAS AF: 0.993

Gnomad SAS AF: 0.863

Gnomad FIN AF: 0.907

Gnomad MID AF: 0.896

Gnomad NFE AF: 0.850

Gnomad OTH AF: 0.881

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

GnomAD4 genome AF: 0.884 AC: 134540 AN: 152166 Hom.: 59586 Cov.: 31 AF XY: 0.888 AC XY: 66032 AN XY: 74386

Gnomad4 AFR AF: 0.915

Gnomad4 AMR AF: 0.908

Gnomad4 ASJ AF: 0.880

Gnomad4 EAS AF: 0.993

Gnomad4 SAS AF: 0.863

Gnomad4 FIN AF: 0.907

Gnomad4 NFE AF: 0.850

Gnomad4 OTH AF: 0.883

Alfa AF: 0.859 Hom.: 32402

Bravo AF: 0.887

Asia WGS AF: 0.937 AC: 3260 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	0.35
Dann	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6788787; hg19: chr3-116870848;