ENST00000666999.1:n.837+11367A>G

Variant names:

• chr7-45280884-A-G
• rs799701
• ENST00000666999.1:n.837+11367A>G

Variant summary

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

The ENST00000666999.1(ENSG00000286738):​n.837+11367A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.838 in 152,076 control chromosomes in the GnomAD database, including 53,526 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 0.84 (53526 hom., cov: 32)
• Consequence: ENSG00000286738 ENST00000666999.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00300

Genes affected

ENSG00000286738 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.65).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.971 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286738	ENST00000666999.1	n.837+11367A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.838 AC: 127337 AN: 151958 Hom.: 53498 Cov.: 32

Gnomad AFR AF: 0.832

Gnomad AMI AF: 0.837

Gnomad AMR AF: 0.874

Gnomad ASJ AF: 0.851

Gnomad EAS AF: 0.994

Gnomad SAS AF: 0.901

Gnomad FIN AF: 0.796

Gnomad MID AF: 0.829

Gnomad NFE AF: 0.823

Gnomad OTH AF: 0.830

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.838 AC: 127413 AN: 152076 Hom.: 53526 Cov.: 32 AF XY: 0.840 AC XY: 62411 AN XY: 74342

Gnomad4 AFR AF: 0.832

Gnomad4 AMR AF: 0.874

Gnomad4 ASJ AF: 0.851

Gnomad4 EAS AF: 0.994

Gnomad4 SAS AF: 0.901

Gnomad4 FIN AF: 0.796

Gnomad4 NFE AF: 0.823

Gnomad4 OTH AF: 0.832

Alfa AF: 0.823 Hom.: 6042

Bravo AF: 0.843

Asia WGS AF: 0.917 AC: 3190 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	12
DANN	Benign	0.92

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs799701; hg19: chr7-45320483;