1-173208097-C-T

Position:

• chr1-173208097-C-T

Variant summary

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

The XM_011509964.3(TNFSF4):​c.148G>A​(p.Asp50Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0697 in 152,146 control chromosomes in the GnomAD database, including 460 homozygotes. In-silico tool predicts a benign outcome for this variant. 4/4 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.070 (460 hom., cov: 32)
• Consequence: TNFSF4 XM_011509964.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.434

Genes affected

TNFSF4 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.139 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TNFSF4	XM_011509964.3	c.148G>A	p.Asp50Asn	missense_variant	1/4		XP_011508266.2
TNFSF4	XM_047429896.1	c.148-912G>A		intron_variant			XP_047285852.1
TNFSF4	XM_047429902.1	c.19-912G>A		intron_variant			XP_047285858.1

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0698 AC: 10604 AN: 152028 Hom.: 463 Cov.: 32

Gnomad AFR AF: 0.0250

Gnomad AMI AF: 0.0429

Gnomad AMR AF: 0.110

Gnomad ASJ AF: 0.0717

Gnomad EAS AF: 0.148

Gnomad SAS AF: 0.0910

Gnomad FIN AF: 0.0648

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0817

Gnomad OTH AF: 0.0694

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

GnomAD4 genome AF: 0.0697 AC: 10607 AN: 152146 Hom.: 460 Cov.: 32 AF XY: 0.0709 AC XY: 5274 AN XY: 74366

Gnomad4 AFR AF: 0.0250

Gnomad4 AMR AF: 0.110

Gnomad4 ASJ AF: 0.0717

Gnomad4 EAS AF: 0.147

Gnomad4 SAS AF: 0.0915

Gnomad4 FIN AF: 0.0648

Gnomad4 NFE AF: 0.0816

Gnomad4 OTH AF: 0.0710

Alfa AF: 0.0789 Hom.: 61

Bravo AF: 0.0689

Asia WGS AF: 0.111 AC: 384 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	7.2
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs45454293; hg19: chr1-173177236;