rs5743402

Variant names:

• chr8-6879763-T-C
• rs5743402
• ENST00000531701.2:n.602-5359T>C

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.602-5359T>C variant causes a intron 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 ENST00000531701.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.303
• Publications: 2 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=-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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GS1-24F4.2	ENST00000531701.2	n.602-5359T>C		intron_variant	Intron 4 of 4	3
GS1-24F4.2	ENST00000772759.1	n.352-5359T>C		intron_variant	Intron 2 of 2
GS1-24F4.2	ENST00000772760.1	n.794-5359T>C		intron_variant	Intron 4 of 4

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

African (AFR) AF: 0.135 AC: 5604 AN: 41530

American (AMR) AF: 0.121 AC: 1854 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.262 AC: 911 AN: 3472

East Asian (EAS) AF: 0.00771 AC: 40 AN: 5186

South Asian (SAS) AF: 0.267 AC: 1286 AN: 4820

European-Finnish (FIN) AF: 0.190 AC: 2009 AN: 10588

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.188 AC: 12771 AN: 68000

Other (OTH) AF: 0.174 AC: 369 AN: 2116

Alfa AF: 0.177 Hom.: 3673

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
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs5743402; hg19: chr8-6737285;