rs2840317

Positions:

• chr1-173257359-T-A

Variant summary

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

The NR_037845.1(LOC100506023):​n.656-17336A>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.214 in 152,128 control chromosomes in the GnomAD database, including 3,819 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 0.21 (3819 hom., cov: 32)
• Consequence: LOC100506023 NR_037845.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03

Genes affected

LOC100506023 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.311 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC100506023	NR_037845.1	n.656-17336A>T		intron_variant, non_coding_transcript_variant
TNFSF4	XM_047429896.1	c.148-50174A>T		intron_variant			XP_047285852.1
TNFSF4	XM_047429902.1	c.19-50174A>T		intron_variant			XP_047285858.1

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.214 AC: 32505 AN: 152010 Hom.: 3813 Cov.: 32

Gnomad AFR AF: 0.121

Gnomad AMI AF: 0.296

Gnomad AMR AF: 0.318

Gnomad ASJ AF: 0.193

Gnomad EAS AF: 0.244

Gnomad SAS AF: 0.200

Gnomad FIN AF: 0.244

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.241

Gnomad OTH AF: 0.214

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

GnomAD4 genome AF: 0.214 AC: 32528 AN: 152128 Hom.: 3819 Cov.: 32 AF XY: 0.215 AC XY: 16007 AN XY: 74378

Gnomad4 AFR AF: 0.121

Gnomad4 AMR AF: 0.319

Gnomad4 ASJ AF: 0.193

Gnomad4 EAS AF: 0.243

Gnomad4 SAS AF: 0.200

Gnomad4 FIN AF: 0.244

Gnomad4 NFE AF: 0.241

Gnomad4 OTH AF: 0.217

Alfa AF: 0.216 Hom.: 476

Bravo AF: 0.220

Asia WGS AF: 0.216 AC: 751 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.4
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2840317; hg19: chr1-173226498;