rs2055426

chr3-117501497-C-T

Variant summary

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

The XR_924361.3(LOC105374056):n.18177C>T 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 0.395 in 151,764 control chromosomes in the GnomAD database, including 14,558 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 0.40 (14558 hom., cov: 31)
• Consequence: LOC105374056 XR_924361.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0910

Genes affected

LOC105374056 (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 (NFE) allele frequency at 95% confidence interval = 0.555 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105374056	XR_924361.3	n.18177C>T		non_coding_transcript_exon_variant	1/4
LOC105374056	XR_007096021.1	n.18177C>T		non_coding_transcript_exon_variant	1/3

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.396 AC: 59990 AN: 151646 Hom.: 14563 Cov.: 31

Gnomad AFR AF: 0.128

Gnomad AMI AF: 0.371

Gnomad AMR AF: 0.330

Gnomad ASJ AF: 0.515

Gnomad EAS AF: 0.223

Gnomad SAS AF: 0.444

Gnomad FIN AF: 0.498

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.560

Gnomad OTH AF: 0.414

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

GnomAD4 genome AF: 0.395 AC: 59964 AN: 151764 Hom.: 14558 Cov.: 31 AF XY: 0.390 AC XY: 28907 AN XY: 74170

Gnomad4 AFR AF: 0.128

Gnomad4 AMR AF: 0.330

Gnomad4 ASJ AF: 0.515

Gnomad4 EAS AF: 0.222

Gnomad4 SAS AF: 0.444

Gnomad4 FIN AF: 0.498

Gnomad4 NFE AF: 0.560

Gnomad4 OTH AF: 0.409

Alfa AF: 0.515 Hom.: 9775

Bravo AF: 0.367

Asia WGS AF: 0.321 AC: 1118 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	2.9
Dann	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2055426; hg19: chr3-117220344;