rs3813127

chr18-22457634-A-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The XR_007066305.1(LOC124904260):n.12351T>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 0.251 in 152,222 control chromosomes in the GnomAD database, including 5,960 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 0.25 (5960 hom., cov: 33)
• Consequence: LOC124904260 XR_007066305.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.50

Genes affected

LOC124904260 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.2).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.57 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124904260	XR_007066305.1	n.12351T>C		non_coding_transcript_exon_variant	3/3
LOC124904261	XR_007066306.1	n.4840A>G		non_coding_transcript_exon_variant	2/2

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.251 AC: 38207 AN: 152104 Hom.: 5954 Cov.: 33

Gnomad AFR AF: 0.113

Gnomad AMI AF: 0.365

Gnomad AMR AF: 0.433

Gnomad ASJ AF: 0.240

Gnomad EAS AF: 0.587

Gnomad SAS AF: 0.248

Gnomad FIN AF: 0.219

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.273

Gnomad OTH AF: 0.250

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

GnomAD4 genome AF: 0.251 AC: 38232 AN: 152222 Hom.: 5960 Cov.: 33 AF XY: 0.254 AC XY: 18932 AN XY: 74438

Gnomad4 AFR AF: 0.113

Gnomad4 AMR AF: 0.433

Gnomad4 ASJ AF: 0.240

Gnomad4 EAS AF: 0.587

Gnomad4 SAS AF: 0.249

Gnomad4 FIN AF: 0.219

Gnomad4 NFE AF: 0.273

Gnomad4 OTH AF: 0.251

Alfa AF: 0.263 Hom.: 788

Bravo AF: 0.266

Asia WGS AF: 0.378 AC: 1310 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.20
Cadd	Benign	18
Dann	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3813127; hg19: chr18-20037597;