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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000531701.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GS1-24F4.2	ENST00000531701.2	TSL:3	n.602-15439G>A		intron	N/A
	GS1-24F4.2	ENST00000655804.2		n.340-3498G>A		intron	N/A
	GS1-24F4.2	ENST00000657010.1		n.791-189G>A		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2702829;

hg19: chr8-6727205;