rs2001099

Variant names:

• chr6-32415856-G-C
• rs2001099
• ENST00000766247.1:n.282+1486G>C

Variant summary

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

The ENST00000766247.1(ENSG00000299769):​n.282+1486G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.129 in 152,078 control chromosomes in the GnomAD database, including 1,547 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 (1547 hom., cov: 31)
• Consequence: ENSG00000299769 ENST00000766247.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.02
• Publications: 15 publications found

Genes affected

ENSG00000299769 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.171 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
ENSG00000299769	ENST00000766247.1	n.282+1486G>C		intron_variant	Intron 2 of 2
ENSG00000299769	ENST00000766248.1	n.286+1486G>C		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.129 AC: 19565 AN: 151960 Hom.: 1547 Cov.: 31

Gnomad AFR AF: 0.0664

Gnomad AMI AF: 0.104

Gnomad AMR AF: 0.114

Gnomad ASJ AF: 0.0904

Gnomad EAS AF: 0.0394

Gnomad SAS AF: 0.0473

Gnomad FIN AF: 0.205

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.173

Gnomad OTH AF: 0.125

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

GnomAD4 genome AF: 0.129 AC: 19573 AN: 152078 Hom.: 1547 Cov.: 31 AF XY: 0.126 AC XY: 9354 AN XY: 74328

African (AFR) AF: 0.0666 AC: 2763 AN: 41484

American (AMR) AF: 0.113 AC: 1734 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0904 AC: 314 AN: 3472

East Asian (EAS) AF: 0.0392 AC: 203 AN: 5172

South Asian (SAS) AF: 0.0467 AC: 225 AN: 4820

European-Finnish (FIN) AF: 0.205 AC: 2168 AN: 10558

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.173 AC: 11789 AN: 67976

Other (OTH) AF: 0.125 AC: 264 AN: 2104

Alfa AF: 0.152 Hom.: 259

Bravo AF: 0.120

Asia WGS AF: 0.0580 AC: 203 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	7.9
DANN	Benign	0.42
PhyloP100		1.0

Splicing

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

Other links and lift over

dbSNP: rs2001099; hg19: chr6-32383633;