rs6697570

chr1-173284964-T-C

Variant summary

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

The NR_037845.1(LOC100506023):n.656-44941A>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 0.303 in 152,114 control chromosomes in the GnomAD database, including 7,589 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 (7589 hom., cov: 32)
• Consequence: LOC100506023 NR_037845.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.533

Genes affected

LOC100506023 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.389 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC100506023	NR_037845.1	n.656-44941A>G		intron_variant, non_coding_transcript_variant
TNFSF4	XM_047429896.1	c.148-77779A>G		intron_variant
TNFSF4	XM_047429902.1	c.19-77779A>G		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.303 AC: 46016 AN: 151996 Hom.: 7583 Cov.: 32

Gnomad AFR AF: 0.176

Gnomad AMI AF: 0.363

Gnomad AMR AF: 0.397

Gnomad ASJ AF: 0.285

Gnomad EAS AF: 0.267

Gnomad SAS AF: 0.309

Gnomad FIN AF: 0.371

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.350

Gnomad OTH AF: 0.310

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

GnomAD4 genome AF: 0.303 AC: 46049 AN: 152114 Hom.: 7589 Cov.: 32 AF XY: 0.306 AC XY: 22737 AN XY: 74360

Gnomad4 AFR AF: 0.176

Gnomad4 AMR AF: 0.398

Gnomad4 ASJ AF: 0.285

Gnomad4 EAS AF: 0.266

Gnomad4 SAS AF: 0.309

Gnomad4 FIN AF: 0.371

Gnomad4 NFE AF: 0.350

Gnomad4 OTH AF: 0.312

Alfa AF: 0.319 Hom.: 1016

Bravo AF: 0.303

Asia WGS AF: 0.288 AC: 1001 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	3.2
Dann	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6697570; hg19: chr1-173254103;