rs3124787

Variant names:

• chr6-160525417-G-T
• rs3124787
• XR_007059844.1:n.483+4585G>T

Variant summary

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

The XR_007059844.1(LOC124901454):​n.483+4585G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.709 in 152,086 control chromosomes in the GnomAD database, including 39,162 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 0.71 (39162 hom., cov: 33)
• Consequence: LOC124901454 XR_007059844.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.00
• Publications: 5 publications found

Genes affected

LOC124901454 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.855 is higher than 0.05.

Variant Effect in Transcripts

 

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
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.709 AC: 107700 AN: 151968 Hom.: 39125 Cov.: 33

Gnomad AFR AF: 0.862

Gnomad AMI AF: 0.742

Gnomad AMR AF: 0.615

Gnomad ASJ AF: 0.659

Gnomad EAS AF: 0.456

Gnomad SAS AF: 0.558

Gnomad FIN AF: 0.649

Gnomad MID AF: 0.744

Gnomad NFE AF: 0.678

Gnomad OTH AF: 0.677

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

GnomAD4 genome AF: 0.709 AC: 107788 AN: 152086 Hom.: 39162 Cov.: 33 AF XY: 0.702 AC XY: 52180 AN XY: 74336

African (AFR) AF: 0.863 AC: 35816 AN: 41520

American (AMR) AF: 0.614 AC: 9388 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.659 AC: 2285 AN: 3470

East Asian (EAS) AF: 0.456 AC: 2354 AN: 5164

South Asian (SAS) AF: 0.558 AC: 2682 AN: 4810

European-Finnish (FIN) AF: 0.649 AC: 6838 AN: 10536

Middle Eastern (MID) AF: 0.738 AC: 217 AN: 294

European-Non Finnish (NFE) AF: 0.678 AC: 46103 AN: 67988

Other (OTH) AF: 0.676 AC: 1428 AN: 2112

Alfa AF: 0.675 Hom.: 49714

Bravo AF: 0.708

Asia WGS AF: 0.544 AC: 1895 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	0.43
DANN	Benign	0.24
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs3124787; hg19: chr6-160946449; COSMIC: COSV69432091;