rs12046550

chr1-173272733-G-A

Variant summary

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

The NR_037845.1(LOC100506023):n.656-32710C>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 0.211 in 152,046 control chromosomes in the GnomAD database, including 3,706 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 (3706 hom., cov: 32)
• Consequence: LOC100506023 NR_037845.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.855

Genes affected

LOC100506023 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.309 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC100506023	NR_037845.1	n.656-32710C>T		intron_variant, non_coding_transcript_variant
TNFSF4	XM_047429896.1	c.148-65548C>T		intron_variant
TNFSF4	XM_047429902.1	c.19-65548C>T		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.211 AC: 32082 AN: 151928 Hom.: 3700 Cov.: 32

Gnomad AFR AF: 0.120

Gnomad AMI AF: 0.276

Gnomad AMR AF: 0.316

Gnomad ASJ AF: 0.192

Gnomad EAS AF: 0.243

Gnomad SAS AF: 0.200

Gnomad FIN AF: 0.243

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.237

Gnomad OTH AF: 0.210

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

GnomAD4 genome AF: 0.211 AC: 32105 AN: 152046 Hom.: 3706 Cov.: 32 AF XY: 0.212 AC XY: 15780 AN XY: 74288

Gnomad4 AFR AF: 0.120

Gnomad4 AMR AF: 0.317

Gnomad4 ASJ AF: 0.192

Gnomad4 EAS AF: 0.242

Gnomad4 SAS AF: 0.200

Gnomad4 FIN AF: 0.243

Gnomad4 NFE AF: 0.237

Gnomad4 OTH AF: 0.213

Alfa AF: 0.224 Hom.: 846

Bravo AF: 0.217

Asia WGS AF: 0.215 AC: 749 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	2.3
Dann	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12046550; hg19: chr1-173241872;