rs5743418

chr8-6878038-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.226-7084G>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 0.0259 in 590,882 control chromosomes in the GnomAD database, including 418 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 0.021 (71 hom., cov: 32)
  • Exomes 𝑓: 0.028 (347 hom.)
• Consequence: GS1-24F4.2 ENST00000531701.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0860

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=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0679 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.226-7084G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.0211 AC: 3212 AN: 152152 Hom.: 71 Cov.: 32

Gnomad AFR AF: 0.0160

Gnomad AMI AF: 0.0329

Gnomad AMR AF: 0.0169

Gnomad ASJ AF: 0.104

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0739

Gnomad FIN AF: 0.00358

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0209

Gnomad OTH AF: 0.0287

GnomAD4 exome AF: 0.0276 AC: 12105 AN: 438612 Hom.: 347 Cov.: 5 AF XY: 0.0311 AC XY: 7276 AN XY: 233758

Gnomad4 AFR exome AF: 0.0165

Gnomad4 AMR exome AF: 0.0162

Gnomad4 ASJ exome AF: 0.105

Gnomad4 EAS exome AF: 0.000143

Gnomad4 SAS exome AF: 0.0772

Gnomad4 FIN exome AF: 0.00462

Gnomad4 NFE exome AF: 0.0212

Gnomad4 OTH exome AF: 0.0314

GnomAD4 genome AF: 0.0211 AC: 3210 AN: 152270 Hom.: 71 Cov.: 32 AF XY: 0.0215 AC XY: 1601 AN XY: 74448

Gnomad4 AFR AF: 0.0160

Gnomad4 AMR AF: 0.0169

Gnomad4 ASJ AF: 0.104

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.0742

Gnomad4 FIN AF: 0.00358

Gnomad4 NFE AF: 0.0209

Gnomad4 OTH AF: 0.0284

Alfa AF: 0.0236 Hom.: 31

Bravo AF: 0.0207

Asia WGS AF: 0.0220 AC: 77 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	5.4
Dann	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5743418; hg19: chr8-6735560;