rs374499

Variant names:

• chr5-127561368-G-A
• rs374499
• XR_007058924.1:n.4412C>T

Your query was ambiguous. Multiple possible variants found:

• chr5-127561368-G-A
• chr5-127561368-G-C
• chr5-127561368-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_007058924.1(LOC124901058):​n.4412C>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 0.41 in 151,988 control chromosomes in the GnomAD database, including 13,797 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 0.41 (13797 hom., cov: 32)
• Consequence: LOC124901058 XR_007058924.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.691
• Publications: 6 publications found

Genes affected

LOC124901058 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.598 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.410 AC: 62288 AN: 151870 Hom.: 13755 Cov.: 32

Gnomad AFR AF: 0.549

Gnomad AMI AF: 0.143

Gnomad AMR AF: 0.440

Gnomad ASJ AF: 0.416

Gnomad EAS AF: 0.616

Gnomad SAS AF: 0.397

Gnomad FIN AF: 0.289

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.326

Gnomad OTH AF: 0.408

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

GnomAD4 genome AF: 0.410 AC: 62379 AN: 151988 Hom.: 13797 Cov.: 32 AF XY: 0.411 AC XY: 30506 AN XY: 74288

African (AFR) AF: 0.550 AC: 22772 AN: 41394

American (AMR) AF: 0.441 AC: 6740 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.416 AC: 1442 AN: 3468

East Asian (EAS) AF: 0.616 AC: 3183 AN: 5170

South Asian (SAS) AF: 0.396 AC: 1909 AN: 4824

European-Finnish (FIN) AF: 0.289 AC: 3050 AN: 10564

Middle Eastern (MID) AF: 0.449 AC: 132 AN: 294

European-Non Finnish (NFE) AF: 0.326 AC: 22172 AN: 67974

Other (OTH) AF: 0.402 AC: 849 AN: 2110

Alfa AF: 0.350 Hom.: 16658

Bravo AF: 0.431

Asia WGS AF: 0.493 AC: 1716 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.46
DANN	Benign	0.51
PhyloP100		-0.69

Splicing

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

Other links and lift over

dbSNP: rs374499; hg19: chr5-126897060; COSMIC: COSV60197068;