rs5743402

chr8-6879763-T-C

Variant summary

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

The ENST00000531701.1(GS1-24F4.2):n.226-5359T>C 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 0.165 in 152,214 control chromosomes in the GnomAD database, including 2,296 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 0.17 (2296 hom., cov: 33)
• Consequence: GS1-24F4.2 ENST00000531701.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.303

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=-0.81).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.255 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.226-5359T>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.165 AC: 25129 AN: 152096 Hom.: 2295 Cov.: 33

Gnomad AFR AF: 0.135

Gnomad AMI AF: 0.246

Gnomad AMR AF: 0.121

Gnomad ASJ AF: 0.262

Gnomad EAS AF: 0.00770

Gnomad SAS AF: 0.266

Gnomad FIN AF: 0.190

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.188

Gnomad OTH AF: 0.177

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

GnomAD4 genome AF: 0.165 AC: 25134 AN: 152214 Hom.: 2296 Cov.: 33 AF XY: 0.166 AC XY: 12349 AN XY: 74414

Gnomad4 AFR AF: 0.135

Gnomad4 AMR AF: 0.121

Gnomad4 ASJ AF: 0.262

Gnomad4 EAS AF: 0.00771

Gnomad4 SAS AF: 0.267

Gnomad4 FIN AF: 0.190

Gnomad4 NFE AF: 0.188

Gnomad4 OTH AF: 0.174

Alfa AF: 0.174 Hom.: 448

Bravo AF: 0.156

Asia WGS AF: 0.113 AC: 395 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	3.6
Dann	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5743402; hg19: chr8-6737285;