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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000846551.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000310013	ENST00000846551.1		n.115-526A>G		intron	N/A
	ENSG00000310013	ENST00000846552.1		n.368-526A>G		intron	N/A
	ENSG00000310013	ENST00000846553.1		n.553-526A>G		intron	N/A

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 v4.9

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;