rs10489265

Positions:

• chr1-173266926-A-C

Variant summary

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

The NR_037845.1(LOC100506023):​n.656-26903T>G 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 0.213 in 152,036 control chromosomes in the GnomAD database, including 3,767 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 (3767 hom., cov: 32)
• Consequence: LOC100506023 NR_037845.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0360

Genes affected

LOC100506023 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• 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.656-26903T>G		intron_variant, non_coding_transcript_variant
TNFSF4	XM_047429896.1	c.148-59741T>G		intron_variant			XP_047285852.1
TNFSF4	XM_047429902.1	c.19-59741T>G		intron_variant			XP_047285858.1

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.213 AC: 32332 AN: 151918 Hom.: 3761 Cov.: 32

Gnomad AFR AF: 0.121

Gnomad AMI AF: 0.293

Gnomad AMR AF: 0.317

Gnomad ASJ AF: 0.192

Gnomad EAS AF: 0.244

Gnomad SAS AF: 0.200

Gnomad FIN AF: 0.244

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.239

Gnomad OTH AF: 0.211

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

GnomAD4 genome AF: 0.213 AC: 32355 AN: 152036 Hom.: 3767 Cov.: 32 AF XY: 0.214 AC XY: 15908 AN XY: 74328

Gnomad4 AFR AF: 0.121

Gnomad4 AMR AF: 0.318

Gnomad4 ASJ AF: 0.192

Gnomad4 EAS AF: 0.243

Gnomad4 SAS AF: 0.200

Gnomad4 FIN AF: 0.244

Gnomad4 NFE AF: 0.239

Gnomad4 OTH AF: 0.213

Alfa AF: 0.234 Hom.: 8481

Bravo AF: 0.219

Asia WGS AF: 0.215 AC: 746 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.5
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10489265; hg19: chr1-173236065;