rs3124787

chr6-160525417-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_007059844.1(LOC124901454):n.483+4585G>T variant causes a intron, non coding transcript 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.00

Genes affected

LOC124901454 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LOC124901454	XR_007059844.1	n.483+4585G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.863

Gnomad4 AMR AF: 0.614

Gnomad4 ASJ AF: 0.659

Gnomad4 EAS AF: 0.456

Gnomad4 SAS AF: 0.558

Gnomad4 FIN AF: 0.649

Gnomad4 NFE AF: 0.678

Gnomad4 OTH AF: 0.676

Alfa AF: 0.674 Hom.: 36565

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

Splicing

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

Publications

LitVar

Other links and lift over

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