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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124901454	XR_007059844.1	n.483+4585G>T		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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;