rs1367807

Positions:

• chr8-63469554-G-C

Variant summary

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

The NR_125825.1(LOC102724612):​n.2562G>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 0.87 in 152,244 control chromosomes in the GnomAD database, including 57,837 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 0.87 (57837 hom., cov: 33)
  • Failed GnomAD Quality Control
• Consequence: LOC102724612 NR_125825.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.68

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.952 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC102724612	NR_125825.1	n.2562G>C		non_coding_transcript_exon_variant	2/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000518739.1	n.2562G>C		non_coding_transcript_exon_variant	2/4	1
	ENST00000522265.6	n.221+425C>G		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.870 AC: 132289 AN: 152126 Hom.: 57779 Cov.: 33

Gnomad AFR AF: 0.960

Gnomad AMI AF: 0.744

Gnomad AMR AF: 0.897

Gnomad ASJ AF: 0.779

Gnomad EAS AF: 0.954

Gnomad SAS AF: 0.937

Gnomad FIN AF: 0.796

Gnomad MID AF: 0.873

Gnomad NFE AF: 0.815

Gnomad OTH AF: 0.870

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.870 AC: 132405 AN: 152244 Hom.: 57837 Cov.: 33 AF XY: 0.871 AC XY: 64823 AN XY: 74426

Gnomad4 AFR AF: 0.960

Gnomad4 AMR AF: 0.897

Gnomad4 ASJ AF: 0.779

Gnomad4 EAS AF: 0.954

Gnomad4 SAS AF: 0.937

Gnomad4 FIN AF: 0.796

Gnomad4 NFE AF: 0.815

Gnomad4 OTH AF: 0.871

Alfa AF: 0.848 Hom.: 6802

Bravo AF: 0.880

Asia WGS AF: 0.937 AC: 3259 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.49
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1367807; hg19: chr8-64382112;