rs2472143

Variant names:

• chr8-6880261-C-T
• rs2472143
• ENST00000531701.1:n.226-4861C>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.226-4861C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.758 in 152,154 control chromosomes in the GnomAD database, including 44,558 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 0.76 (44558 hom., cov: 32)
• Consequence: GS1-24F4.2 ENST00000531701.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.80

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=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.894 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.226-4861C>T		intron_variant	Intron 2 of 2	3

Frequencies

GnomAD3 genomes AF: 0.758 AC: 115289 AN: 152034 Hom.: 44508 Cov.: 32

Gnomad AFR AF: 0.901

Gnomad AMI AF: 0.667

Gnomad AMR AF: 0.718

Gnomad ASJ AF: 0.695

Gnomad EAS AF: 0.547

Gnomad SAS AF: 0.740

Gnomad FIN AF: 0.811

Gnomad MID AF: 0.639

Gnomad NFE AF: 0.696

Gnomad OTH AF: 0.719

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

GnomAD4 genome AF: 0.758 AC: 115394 AN: 152154 Hom.: 44558 Cov.: 32 AF XY: 0.760 AC XY: 56581 AN XY: 74408

Gnomad4 AFR AF: 0.901

Gnomad4 AMR AF: 0.719

Gnomad4 ASJ AF: 0.695

Gnomad4 EAS AF: 0.547

Gnomad4 SAS AF: 0.740

Gnomad4 FIN AF: 0.811

Gnomad4 NFE AF: 0.695

Gnomad4 OTH AF: 0.714

Alfa AF: 0.743 Hom.: 5270

Bravo AF: 0.757

Asia WGS AF: 0.633 AC: 2201 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.59
DANN	Benign	0.21

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2472143; hg19: chr8-6737783;