1-173209324-C-T

Variant summary

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

The XM_047429896.1(TNFSF4):c.148-2139G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.569 in 152,002 control chromosomes in the GnomAD database, including 26,309 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 0.57 (26309 hom., cov: 32)
• Consequence: TNFSF4 XM_047429896.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.13

Genes affected

TNFSF4 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.789 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TNFSF4	XM_047429896.1	c.148-2139G>A		intron_variant
TNFSF4	XM_047429902.1	c.19-2139G>A		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.568 AC: 86323 AN: 151884 Hom.: 26252 Cov.: 32

Gnomad AFR AF: 0.795

Gnomad AMI AF: 0.472

Gnomad AMR AF: 0.606

Gnomad ASJ AF: 0.472

Gnomad EAS AF: 0.420

Gnomad SAS AF: 0.461

Gnomad FIN AF: 0.438

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.467

Gnomad OTH AF: 0.553

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

GnomAD4 genome AF: 0.569 AC: 86437 AN: 152002 Hom.: 26309 Cov.: 32 AF XY: 0.567 AC XY: 42110 AN XY: 74274

Gnomad4 AFR AF: 0.796

Gnomad4 AMR AF: 0.606

Gnomad4 ASJ AF: 0.472

Gnomad4 EAS AF: 0.419

Gnomad4 SAS AF: 0.461

Gnomad4 FIN AF: 0.438

Gnomad4 NFE AF: 0.467

Gnomad4 OTH AF: 0.556

Alfa AF: 0.492 Hom.: 25511

Bravo AF: 0.591

Asia WGS AF: 0.481 AC: 1669 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	0.0030
Dann	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1234315; hg19: chr1-173178463;