chr4-54101191-C-A

Variant names:

• chr4-54101191-C-A
• rs2278141
• NM_133267.3:c.574+273C>A

Variant summary

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

The NM_133267.3(GSX2):​c.574+273C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.554 in 152,116 control chromosomes in the GnomAD database, including 25,011 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 0.55 (25011 hom., cov: 32)
• Consequence: GSX2 NM_133267.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0250

Genes affected

GSX2 (HGNC:24959): (GS homeobox 2) Enables DNA-binding transcription factor activity, RNA polymerase II-specific and sequence-specific double-stranded DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to act upstream of or within several processes, including nervous system development; positive regulation of Notch signaling pathway; and regulation of respiratory gaseous exchange by nervous system process. Located in cytoplasm and nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000282278 (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 (EAS) allele frequency at 95% confidence interval = 0.811 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GSX2	NM_133267.3	c.574+273C>A		intron_variant	Intron 1 of 1	ENST00000326902.7	NP_573574.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GSX2	ENST00000326902.7	c.574+273C>A		intron_variant	Intron 1 of 1	1	NM_133267.3	ENSP00000319118.2
ENSG00000282278	ENST00000507166.5	c.1018-173734C>A		intron_variant	Intron 12 of 23	2		ENSP00000423325.1
GSX2	ENST00000503800.1	c.364-391C>A		intron_variant	Intron 1 of 1	5		ENSP00000422213.1
GSX2	ENST00000507839.1	n.115-391C>A		intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes AF: 0.555 AC: 84309 AN: 151996 Hom.: 24996 Cov.: 32

Gnomad AFR AF: 0.340

Gnomad AMI AF: 0.737

Gnomad AMR AF: 0.667

Gnomad ASJ AF: 0.554

Gnomad EAS AF: 0.832

Gnomad SAS AF: 0.650

Gnomad FIN AF: 0.645

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.616

Gnomad OTH AF: 0.566

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

GnomAD4 genome AF: 0.554 AC: 84340 AN: 152116 Hom.: 25011 Cov.: 32 AF XY: 0.560 AC XY: 41667 AN XY: 74362

Gnomad4 AFR AF: 0.340

Gnomad4 AMR AF: 0.668

Gnomad4 ASJ AF: 0.554

Gnomad4 EAS AF: 0.832

Gnomad4 SAS AF: 0.649

Gnomad4 FIN AF: 0.645

Gnomad4 NFE AF: 0.616

Gnomad4 OTH AF: 0.568

Alfa AF: 0.575 Hom.: 3773

Bravo AF: 0.549

Asia WGS AF: 0.696 AC: 2419 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	1.8
DANN	Benign	0.55

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs2278141; hg19: chr4-54967358;