rs5743404

Variant names:

• chr8-6879599-G-A
• rs5743404
• ENST00000531701.2:n.602-5523G>A

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.602-5523G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.592 in 151,774 control chromosomes in the GnomAD database, including 27,481 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 0.59 (27481 hom., cov: 30)
• Consequence: GS1-24F4.2 ENST00000531701.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.519
• Publications: 6 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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.649 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.602-5523G>A		intron_variant	Intron 4 of 4	3
GS1-24F4.2	ENST00000772759.1	n.352-5523G>A		intron_variant	Intron 2 of 2
GS1-24F4.2	ENST00000772760.1	n.794-5523G>A		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.592 AC: 89757 AN: 151656 Hom.: 27475 Cov.: 30

Gnomad AFR AF: 0.433

Gnomad AMI AF: 0.634

Gnomad AMR AF: 0.633

Gnomad ASJ AF: 0.574

Gnomad EAS AF: 0.510

Gnomad SAS AF: 0.596

Gnomad FIN AF: 0.798

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.654

Gnomad OTH AF: 0.575

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

GnomAD4 genome AF: 0.592 AC: 89784 AN: 151774 Hom.: 27481 Cov.: 30 AF XY: 0.597 AC XY: 44289 AN XY: 74166

African (AFR) AF: 0.432 AC: 17883 AN: 41350

American (AMR) AF: 0.634 AC: 9680 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.574 AC: 1991 AN: 3466

East Asian (EAS) AF: 0.510 AC: 2586 AN: 5074

South Asian (SAS) AF: 0.596 AC: 2858 AN: 4796

European-Finnish (FIN) AF: 0.798 AC: 8432 AN: 10572

Middle Eastern (MID) AF: 0.486 AC: 142 AN: 292

European-Non Finnish (NFE) AF: 0.654 AC: 44435 AN: 67936

Other (OTH) AF: 0.570 AC: 1199 AN: 2102

Alfa AF: 0.629 Hom.: 49802

Bravo AF: 0.573

Asia WGS AF: 0.527 AC: 1835 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.4
DANN	Benign	0.32
PhyloP100		-0.52

Splicing

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

Other links and lift over

dbSNP: rs5743404; hg19: chr8-6737121;