rs12750070

chr1-173280633-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.656-40610G>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 0.298 in 151,924 control chromosomes in the GnomAD database, including 7,323 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 0.30 (7323 hom., cov: 32)
• Consequence: LOC100506023 NR_037845.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.368

Genes affected

LOC100506023 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.388 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC100506023	NR_037845.1	n.656-40610G>A		intron_variant, non_coding_transcript_variant
TNFSF4	XM_047429896.1	c.148-73448G>A		intron_variant
TNFSF4	XM_047429902.1	c.19-73448G>A		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.298 AC: 45208 AN: 151806 Hom.: 7317 Cov.: 32

Gnomad AFR AF: 0.172

Gnomad AMI AF: 0.365

Gnomad AMR AF: 0.396

Gnomad ASJ AF: 0.279

Gnomad EAS AF: 0.268

Gnomad SAS AF: 0.310

Gnomad FIN AF: 0.349

Gnomad MID AF: 0.274

Gnomad NFE AF: 0.346

Gnomad OTH AF: 0.308

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

GnomAD4 genome AF: 0.298 AC: 45241 AN: 151924 Hom.: 7323 Cov.: 32 AF XY: 0.300 AC XY: 22273 AN XY: 74220

Gnomad4 AFR AF: 0.172

Gnomad4 AMR AF: 0.397

Gnomad4 ASJ AF: 0.279

Gnomad4 EAS AF: 0.267

Gnomad4 SAS AF: 0.310

Gnomad4 FIN AF: 0.349

Gnomad4 NFE AF: 0.346

Gnomad4 OTH AF: 0.310

Alfa AF: 0.328 Hom.: 2878

Bravo AF: 0.300

Asia WGS AF: 0.287 AC: 998 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	0.26
Dann	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12750070; hg19: chr1-173249772;