rs5743399

Positions:

• chr8-6880123-G-A
• chr8-6880123-G-T

Variant summary

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

The ENST00000531701.1(GS1-24F4.2):​n.226-4999G>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 0.303 in 152,058 control chromosomes in the GnomAD database, including 7,128 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 0.30 (7128 hom., cov: 32)
• Consequence: GS1-24F4.2 ENST00000531701.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.67

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=-1.06).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.328 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GS1-24F4.2	ENST00000531701.1	n.226-4999G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.303 AC: 46086 AN: 151940 Hom.: 7126 Cov.: 32

Gnomad AFR AF: 0.320

Gnomad AMI AF: 0.313

Gnomad AMR AF: 0.336

Gnomad ASJ AF: 0.283

Gnomad EAS AF: 0.148

Gnomad SAS AF: 0.185

Gnomad FIN AF: 0.288

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.310

Gnomad OTH AF: 0.298

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

GnomAD4 genome AF: 0.303 AC: 46118 AN: 152058 Hom.: 7128 Cov.: 32 AF XY: 0.299 AC XY: 22217 AN XY: 74320

Gnomad4 AFR AF: 0.320

Gnomad4 AMR AF: 0.336

Gnomad4 ASJ AF: 0.283

Gnomad4 EAS AF: 0.148

Gnomad4 SAS AF: 0.185

Gnomad4 FIN AF: 0.288

Gnomad4 NFE AF: 0.310

Gnomad4 OTH AF: 0.299

Alfa AF: 0.181 Hom.: 352

Bravo AF: 0.312

Asia WGS AF: 0.218 AC: 758 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	2.0
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5743399; hg19: chr8-6737645;