rs2702829

Variant names:

• chr8-6869683-G-A
• rs2702829
• ENST00000531701.2:n.602-15439G>A

Variant summary

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

The ENST00000531701.2(GS1-24F4.2):​n.602-15439G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.653 in 152,100 control chromosomes in the GnomAD database, including 32,825 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 0.65 (32825 hom., cov: 33)
• Consequence: GS1-24F4.2 ENST00000531701.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.830
• Publications: 2 publications found

Genes affected

GS1-24F4.2 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.71 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
GS1-24F4.2	ENST00000531701.2	n.602-15439G>A		intron_variant	Intron 4 of 4	3
GS1-24F4.2	ENST00000655804.2	n.340-3498G>A		intron_variant	Intron 2 of 2
GS1-24F4.2	ENST00000657010.1	n.791-189G>A		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.653 AC: 99252 AN: 151982 Hom.: 32808 Cov.: 33

Gnomad AFR AF: 0.572

Gnomad AMI AF: 0.691

Gnomad AMR AF: 0.671

Gnomad ASJ AF: 0.687

Gnomad EAS AF: 0.529

Gnomad SAS AF: 0.730

Gnomad FIN AF: 0.802

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.678

Gnomad OTH AF: 0.633

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

GnomAD4 genome AF: 0.653 AC: 99315 AN: 152100 Hom.: 32825 Cov.: 33 AF XY: 0.659 AC XY: 48988 AN XY: 74372

African (AFR) AF: 0.572 AC: 23706 AN: 41480

American (AMR) AF: 0.672 AC: 10261 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.687 AC: 2386 AN: 3472

East Asian (EAS) AF: 0.528 AC: 2727 AN: 5162

South Asian (SAS) AF: 0.730 AC: 3522 AN: 4822

European-Finnish (FIN) AF: 0.802 AC: 8479 AN: 10578

Middle Eastern (MID) AF: 0.554 AC: 163 AN: 294

European-Non Finnish (NFE) AF: 0.678 AC: 46114 AN: 67990

Other (OTH) AF: 0.629 AC: 1327 AN: 2110

Alfa AF: 0.659 Hom.: 4882

Bravo AF: 0.638

Asia WGS AF: 0.595 AC: 2070 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	1.2
DANN	Benign	0.66
PhyloP100		-0.83

Splicing

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

Other links and lift over

dbSNP: rs2702829; hg19: chr8-6727205;