rs4916315

Positions:

• chr1-173246233-C-T

Variant summary

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

The NR_037845.1(LOC100506023):​n.656-6210G>A 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 0.211 in 151,956 control chromosomes in the GnomAD database, including 3,701 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 (3701 hom., cov: 31)
• Consequence: LOC100506023 NR_037845.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.938

Genes affected

LOC100506023 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.31 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC100506023	NR_037845.1	n.656-6210G>A		intron_variant, non_coding_transcript_variant
TNFSF4	XM_047429896.1	c.148-39048G>A		intron_variant
TNFSF4	XM_047429902.1	c.19-39048G>A		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.211 AC: 32076 AN: 151838 Hom.: 3695 Cov.: 31

Gnomad AFR AF: 0.119

Gnomad AMI AF: 0.275

Gnomad AMR AF: 0.317

Gnomad ASJ AF: 0.193

Gnomad EAS AF: 0.243

Gnomad SAS AF: 0.201

Gnomad FIN AF: 0.244

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.237

Gnomad OTH AF: 0.211

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

GnomAD4 genome AF: 0.211 AC: 32099 AN: 151956 Hom.: 3701 Cov.: 31 AF XY: 0.213 AC XY: 15803 AN XY: 74276

Gnomad4 AFR AF: 0.119

Gnomad4 AMR AF: 0.317

Gnomad4 ASJ AF: 0.193

Gnomad4 EAS AF: 0.242

Gnomad4 SAS AF: 0.201

Gnomad4 FIN AF: 0.244

Gnomad4 NFE AF: 0.237

Gnomad4 OTH AF: 0.214

Alfa AF: 0.213 Hom.: 471

Bravo AF: 0.217

Asia WGS AF: 0.213 AC: 742 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.89
DANN	Benign	0.25

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4916315; hg19: chr1-173215372;