rs5743399

Variant names:

• chr8-6880123-G-A
• rs5743399
• ENST00000531701.2:n.602-4999G>A

Your query was ambiguous. Multiple possible variants found:

• chr8-6880123-G-A
• chr8-6880123-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000531701.2(GS1-24F4.2):​n.602-4999G>A variant causes a intron 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 ENST00000531701.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.67
• Publications: 7 publications found

Genes affected

GS1-24F4.2 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GS1-24F4.2	ENST00000531701.2	n.602-4999G>A		intron_variant	Intron 4 of 4	3
GS1-24F4.2	ENST00000772759.1	n.352-4999G>A		intron_variant	Intron 2 of 2
GS1-24F4.2	ENST00000772760.1	n.794-4999G>A		intron_variant	Intron 4 of 4

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

African (AFR) AF: 0.320 AC: 13254 AN: 41448

American (AMR) AF: 0.336 AC: 5129 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.283 AC: 981 AN: 3468

East Asian (EAS) AF: 0.148 AC: 768 AN: 5180

South Asian (SAS) AF: 0.185 AC: 890 AN: 4822

European-Finnish (FIN) AF: 0.288 AC: 3046 AN: 10560

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.310 AC: 21054 AN: 67990

Other (OTH) AF: 0.299 AC: 630 AN: 2110

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
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs5743399; hg19: chr8-6737645;