rs2472143

Variant names:

• chr8-6880261-C-T
• rs2472143
• ENST00000531701.2:n.602-4861C>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.602-4861C>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 ENST00000531701.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.80
• Publications: 0 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=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.894 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000531701.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GS1-24F4.2	ENST00000531701.2	TSL:3	n.602-4861C>T		intron	N/A
	GS1-24F4.2	ENST00000772759.1		n.352-4861C>T		intron	N/A
	GS1-24F4.2	ENST00000772760.1		n.794-4861C>T		intron	N/A

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

African (AFR) AF: 0.901 AC: 37438 AN: 41532

American (AMR) AF: 0.719 AC: 10972 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.695 AC: 2412 AN: 3470

East Asian (EAS) AF: 0.547 AC: 2832 AN: 5176

South Asian (SAS) AF: 0.740 AC: 3565 AN: 4816

European-Finnish (FIN) AF: 0.811 AC: 8596 AN: 10600

Middle Eastern (MID) AF: 0.643 AC: 189 AN: 294

European-Non Finnish (NFE) AF: 0.695 AC: 47275 AN: 67974

Other (OTH) AF: 0.714 AC: 1507 AN: 2112

Alfa AF: 0.749 Hom.: 5590

Bravo AF: 0.757

Asia WGS AF: 0.633 AC: 2201 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.59
DANN	Benign	0.21
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs2472143; hg19: chr8-6737783;