rs3813127

Variant names:

• chr18-22457634-A-G
• rs3813127
• XR_007066305.1:n.12351T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

Genes affected

LOC124904260 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LOC124904260	XR_007066305.1	n.12351T>C		non_coding_transcript_exon_variant	Exon 3 of 3
LOC124904261	XR_007066306.1	n.4840A>G		non_coding_transcript_exon_variant	Exon 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000310013	ENST00000846551.1	n.115-526A>G		intron_variant	Intron 1 of 1
ENSG00000310013	ENST00000846552.1	n.368-526A>G		intron_variant	Intron 2 of 2
ENSG00000310013	ENST00000846553.1	n.553-526A>G		intron_variant	Intron 3 of 3

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

African (AFR) AF: 0.113 AC: 4685 AN: 41554

American (AMR) AF: 0.433 AC: 6625 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.240 AC: 835 AN: 3472

East Asian (EAS) AF: 0.587 AC: 3038 AN: 5174

South Asian (SAS) AF: 0.249 AC: 1204 AN: 4826

European-Finnish (FIN) AF: 0.219 AC: 2323 AN: 10588

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.273 AC: 18596 AN: 68008

Other (OTH) AF: 0.251 AC: 530 AN: 2110

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
PhyloP100		3.5

Splicing

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

Other links and lift over

dbSNP: rs3813127; hg19: chr18-20037597;