3-99333303-A-G

Variant summary

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

The XR_924266.2(LOC105374004):n.201-3426T>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 0.497 in 150,680 control chromosomes in the GnomAD database, including 22,820 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 0.50 (22820 hom., cov: 30)
• Consequence: LOC105374004 XR_924266.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.04

Genes affected

LOC105374004 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.655 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105374004	XR_924266.2	n.201-3426T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.497 AC: 74914 AN: 150594 Hom.: 22841 Cov.: 30

Gnomad AFR AF: 0.133

Gnomad AMI AF: 0.575

Gnomad AMR AF: 0.559

Gnomad ASJ AF: 0.809

Gnomad EAS AF: 0.454

Gnomad SAS AF: 0.556

Gnomad FIN AF: 0.669

Gnomad MID AF: 0.694

Gnomad NFE AF: 0.660

Gnomad OTH AF: 0.536

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

GnomAD4 genome AF: 0.497 AC: 74878 AN: 150680 Hom.: 22820 Cov.: 30 AF XY: 0.499 AC XY: 36694 AN XY: 73496

Gnomad4 AFR AF: 0.133

Gnomad4 AMR AF: 0.558

Gnomad4 ASJ AF: 0.809

Gnomad4 EAS AF: 0.454

Gnomad4 SAS AF: 0.555

Gnomad4 FIN AF: 0.669

Gnomad4 NFE AF: 0.660

Gnomad4 OTH AF: 0.534

Alfa AF: 0.647 Hom.: 62717

Bravo AF: 0.475

Asia WGS AF: 0.464 AC: 1612 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	6.5
Dann	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9861463; hg19: chr3-99052147;