rs704840

Positions:

• chr1-173257056-T-G

Variant summary

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

The NR_037845.1(LOC100506023):​n.656-17033A>C 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 0.291 in 152,160 control chromosomes in the GnomAD database, including 6,594 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 0.29 (6594 hom., cov: 33)
• Consequence: LOC100506023 NR_037845.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0900

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 (EAS) allele frequency at 95% confidence interval = 0.365 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC100506023	NR_037845.1	n.656-17033A>C		intron_variant, non_coding_transcript_variant
TNFSF4	XM_047429896.1	c.148-49871A>C		intron_variant			XP_047285852.1
TNFSF4	XM_047429902.1	c.19-49871A>C		intron_variant			XP_047285858.1

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.291 AC: 44306 AN: 152042 Hom.: 6581 Cov.: 33

Gnomad AFR AF: 0.263

Gnomad AMI AF: 0.318

Gnomad AMR AF: 0.372

Gnomad ASJ AF: 0.236

Gnomad EAS AF: 0.374

Gnomad SAS AF: 0.254

Gnomad FIN AF: 0.292

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.290

Gnomad OTH AF: 0.281

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

GnomAD4 genome AF: 0.291 AC: 44344 AN: 152160 Hom.: 6594 Cov.: 33 AF XY: 0.293 AC XY: 21767 AN XY: 74386

Gnomad4 AFR AF: 0.263

Gnomad4 AMR AF: 0.373

Gnomad4 ASJ AF: 0.236

Gnomad4 EAS AF: 0.373

Gnomad4 SAS AF: 0.254

Gnomad4 FIN AF: 0.292

Gnomad4 NFE AF: 0.290

Gnomad4 OTH AF: 0.285

Alfa AF: 0.289 Hom.: 13213

Bravo AF: 0.300

Asia WGS AF: 0.313 AC: 1089 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	4.1
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs704840; hg19: chr1-173226195;