rs5743409

Variant names:

• chr8-6879098-C-A
• rs5743409
• ENST00000531701.1:n.226-6024C>A

Your query was ambiguous. Multiple possible variants found:

• chr8-6879098-C-A
• chr8-6879098-C-G
• chr8-6879098-C-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.226-6024C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.406 in 150,954 control chromosomes in the GnomAD database, including 12,763 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 0.41 (12763 hom., cov: 28)
• Consequence: GS1-24F4.2 ENST00000531701.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.24

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=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.437 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GS1-24F4.2	ENST00000531701.1	n.226-6024C>A		intron_variant	Intron 2 of 2	3

Frequencies

GnomAD3 genomes AF: 0.406 AC: 61208 AN: 150836 Hom.: 12760 Cov.: 28

Gnomad AFR AF: 0.308

Gnomad AMI AF: 0.383

Gnomad AMR AF: 0.395

Gnomad ASJ AF: 0.387

Gnomad EAS AF: 0.393

Gnomad SAS AF: 0.442

Gnomad FIN AF: 0.573

Gnomad MID AF: 0.376

Gnomad NFE AF: 0.441

Gnomad OTH AF: 0.400

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

GnomAD4 genome AF: 0.406 AC: 61218 AN: 150954 Hom.: 12763 Cov.: 28 AF XY: 0.411 AC XY: 30306 AN XY: 73722

Gnomad4 AFR AF: 0.308

Gnomad4 AMR AF: 0.396

Gnomad4 ASJ AF: 0.387

Gnomad4 EAS AF: 0.392

Gnomad4 SAS AF: 0.442

Gnomad4 FIN AF: 0.573

Gnomad4 NFE AF: 0.441

Gnomad4 OTH AF: 0.395

Alfa AF: 0.421 Hom.: 1686

Bravo AF: 0.386

Asia WGS AF: 0.359 AC: 1249 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.35
DANN	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5743409; hg19: chr8-6736620;