rs1695693

chr8-117313702-A-Gchr8-117313702-A-T

Variant summary

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

The ENST00000671266.1(ENSG00000286308):n.47-1996A>G 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 0.714 in 152,100 control chromosomes in the GnomAD database, including 39,628 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 (39628 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: ENST00000671266.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.56

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.858 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105375716	XR_007061067.1	n.559+127258T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000671266.1	n.47-1996A>G		intron_variant, non_coding_transcript_variant
	ENST00000517043.1			downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.713 AC: 108419 AN: 151982 Hom.: 39581 Cov.: 32

Gnomad AFR AF: 0.865

Gnomad AMI AF: 0.577

Gnomad AMR AF: 0.689

Gnomad ASJ AF: 0.687

Gnomad EAS AF: 0.857

Gnomad SAS AF: 0.784

Gnomad FIN AF: 0.688

Gnomad MID AF: 0.718

Gnomad NFE AF: 0.618

Gnomad OTH AF: 0.694

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: 0.714 AC: 108525 AN: 152100 Hom.: 39628 Cov.: 32 AF XY: 0.718 AC XY: 53372 AN XY: 74344

Gnomad4 AFR AF: 0.865

Gnomad4 AMR AF: 0.689

Gnomad4 ASJ AF: 0.687

Gnomad4 EAS AF: 0.858

Gnomad4 SAS AF: 0.785

Gnomad4 FIN AF: 0.688

Gnomad4 NFE AF: 0.618

Gnomad4 OTH AF: 0.698

Alfa AF: 0.638 Hom.: 57795

Bravo AF: 0.718

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	0.88
Dann	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1695693; hg19: chr8-118325941;