rs10489266

chr1-173209314-A-G

Variant summary

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

The XM_047429896.1(TNFSF4):c.148-2129T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0776 in 152,236 control chromosomes in the GnomAD database, including 535 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 0.078 (535 hom., cov: 32)
• Consequence: TNFSF4 XM_047429896.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.280

Genes affected

TNFSF4 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.108 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TNFSF4	XM_047429896.1	c.148-2129T>C		intron_variant
TNFSF4	XM_047429902.1	c.19-2129T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0776 AC: 11802 AN: 152118 Hom.: 536 Cov.: 32

Gnomad AFR AF: 0.0468

Gnomad AMI AF: 0.0570

Gnomad AMR AF: 0.0778

Gnomad ASJ AF: 0.0931

Gnomad EAS AF: 0.0239

Gnomad SAS AF: 0.116

Gnomad FIN AF: 0.0890

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.0945

Gnomad OTH AF: 0.0923

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

GnomAD4 genome AF: 0.0776 AC: 11806 AN: 152236 Hom.: 535 Cov.: 32 AF XY: 0.0780 AC XY: 5805 AN XY: 74434

Gnomad4 AFR AF: 0.0468

Gnomad4 AMR AF: 0.0777

Gnomad4 ASJ AF: 0.0931

Gnomad4 EAS AF: 0.0239

Gnomad4 SAS AF: 0.116

Gnomad4 FIN AF: 0.0890

Gnomad4 NFE AF: 0.0945

Gnomad4 OTH AF: 0.0937

Alfa AF: 0.0939 Hom.: 996

Bravo AF: 0.0749

Asia WGS AF: 0.0820 AC: 285 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	6.8
Dann	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10489266; hg19: chr1-173178453;