rs12049190

Positions:

• chr1-173278118-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.656-38095A>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 0.332 in 151,874 control chromosomes in the GnomAD database, including 8,591 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 0.33 (8591 hom., cov: 31)
• Consequence: LOC100506023 NR_037845.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.395

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 = 0.401 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC100506023	NR_037845.1	n.656-38095A>T		intron_variant, non_coding_transcript_variant
TNFSF4	XM_047429896.1	c.148-70933A>T		intron_variant			XP_047285852.1
TNFSF4	XM_047429902.1	c.19-70933A>T		intron_variant			XP_047285858.1

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.332 AC: 50452 AN: 151756 Hom.: 8583 Cov.: 31

Gnomad AFR AF: 0.281

Gnomad AMI AF: 0.363

Gnomad AMR AF: 0.409

Gnomad ASJ AF: 0.284

Gnomad EAS AF: 0.268

Gnomad SAS AF: 0.310

Gnomad FIN AF: 0.370

Gnomad MID AF: 0.274

Gnomad NFE AF: 0.350

Gnomad OTH AF: 0.329

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

GnomAD4 genome AF: 0.332 AC: 50488 AN: 151874 Hom.: 8591 Cov.: 31 AF XY: 0.335 AC XY: 24837 AN XY: 74204

Gnomad4 AFR AF: 0.281

Gnomad4 AMR AF: 0.409

Gnomad4 ASJ AF: 0.284

Gnomad4 EAS AF: 0.267

Gnomad4 SAS AF: 0.309

Gnomad4 FIN AF: 0.370

Gnomad4 NFE AF: 0.350

Gnomad4 OTH AF: 0.331

Alfa AF: 0.337 Hom.: 1094

Bravo AF: 0.337

Asia WGS AF: 0.292 AC: 1014 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	2.4
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12049190; hg19: chr1-173247257;