rs1695693

Variant names:

• chr8-117313702-A-G
• rs1695693
• ENST00000671266.1:n.47-1996A>G

Your query was ambiguous. Multiple possible variants found:

• chr8-117313702-A-G
• chr8-117313702-A-T

Variant summary

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

The ENST00000671266.1(ENSG00000286308):​n.47-1996A>G variant causes a intron 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: ENSG00000286308 ENST00000671266.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.56
• Publications: 2 publications found

Genes affected

ENSG00000286308 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LOC105375716	XR_007061067.1	n.559+127258T>C		intron_variant	Intron 3 of 5
LOC105375716	XR_007061068.1	n.946+127258T>C		intron_variant	Intron 5 of 7
LOC105375716	XR_928568.4	n.714+127258T>C		intron_variant	Intron 4 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286308	ENST00000671266.1	n.47-1996A>G		intron_variant	Intron 1 of 2
ENSG00000286308	ENST00000754617.1	n.194-1996A>G		intron_variant	Intron 2 of 3
ENSG00000286308	ENST00000754618.1	n.194-1996A>G		intron_variant	Intron 2 of 2
ENSG00000252852	ENST00000517043.1	n.*41A>G		downstream_gene_variant		6

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.714 AC: 108525 AN: 152100 Hom.: 39628 Cov.: 32 AF XY: 0.718 AC XY: 53372 AN XY: 74344

African (AFR) AF: 0.865 AC: 35918 AN: 41510

American (AMR) AF: 0.689 AC: 10524 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.687 AC: 2383 AN: 3470

East Asian (EAS) AF: 0.858 AC: 4438 AN: 5174

South Asian (SAS) AF: 0.785 AC: 3788 AN: 4826

European-Finnish (FIN) AF: 0.688 AC: 7258 AN: 10554

Middle Eastern (MID) AF: 0.724 AC: 213 AN: 294

European-Non Finnish (NFE) AF: 0.618 AC: 42009 AN: 67974

Other (OTH) AF: 0.698 AC: 1468 AN: 2104

Alfa AF: 0.648 Hom.: 124926

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
PhyloP100		-1.6
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs1695693; hg19: chr8-118325941;