rs2702829

Positions:

• chr8-6869683-G-A

Variant summary

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

The ENST00000531701.1(GS1-24F4.2):​n.226-15439G>A variant causes a intron, non coding transcript 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 ENST00000531701.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.830

Genes affected

GS1-24F4.2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GS1-24F4.2	ENST00000531701.1	n.226-15439G>A		intron_variant, non_coding_transcript_variant		3
GS1-24F4.2	ENST00000655804.1	n.323-3498G>A		intron_variant, non_coding_transcript_variant
GS1-24F4.2	ENST00000657010.1	n.791-189G>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.572

Gnomad4 AMR AF: 0.672

Gnomad4 ASJ AF: 0.687

Gnomad4 EAS AF: 0.528

Gnomad4 SAS AF: 0.730

Gnomad4 FIN AF: 0.802

Gnomad4 NFE AF: 0.678

Gnomad4 OTH AF: 0.629

Alfa AF: 0.662 Hom.: 4764

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2702829; hg19: chr8-6727205;