rs3116999

Variant names:

• chr6-33129389-G-C
• rs3116999
• ENST00000782897.1:n.587G>C

Variant summary

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

The ENST00000782897.1(ENSG00000291111):​n.587G>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 0.13 in 152,216 control chromosomes in the GnomAD database, including 1,469 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 0.13 (1469 hom., cov: 31)
• Consequence: ENSG00000291111 ENST00000782897.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.100
• Publications: 10 publications found

Genes affected

ENSG00000291111 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.16 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
ENSG00000291111	ENST00000782897.1	n.587G>C		non_coding_transcript_exon_variant	Exon 4 of 4
ENSG00000291111	ENST00000782901.1	n.311G>C		non_coding_transcript_exon_variant	Exon 3 of 3
ENSG00000291111	ENST00000782902.1	n.1781G>C		non_coding_transcript_exon_variant	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.131 AC: 19851 AN: 152094 Hom.: 1473 Cov.: 31

Gnomad AFR AF: 0.0757

Gnomad AMI AF: 0.0452

Gnomad AMR AF: 0.0949

Gnomad ASJ AF: 0.178

Gnomad EAS AF: 0.134

Gnomad SAS AF: 0.148

Gnomad FIN AF: 0.176

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.162

Gnomad OTH AF: 0.117

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

GnomAD4 genome AF: 0.130 AC: 19861 AN: 152216 Hom.: 1469 Cov.: 31 AF XY: 0.130 AC XY: 9638 AN XY: 74418

African (AFR) AF: 0.0760 AC: 3159 AN: 41544

American (AMR) AF: 0.0949 AC: 1451 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.178 AC: 619 AN: 3472

East Asian (EAS) AF: 0.133 AC: 692 AN: 5188

South Asian (SAS) AF: 0.148 AC: 711 AN: 4820

European-Finnish (FIN) AF: 0.176 AC: 1863 AN: 10580

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.162 AC: 11045 AN: 68002

Other (OTH) AF: 0.116 AC: 246 AN: 2112

Alfa AF: 0.152 Hom.: 984

Bravo AF: 0.120

Asia WGS AF: 0.144 AC: 503 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	7.4
DANN	Benign	0.33
PhyloP100		-0.10

Splicing

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

Other links and lift over

dbSNP: rs3116999; hg19: chr6-33097166;