1-173473779-G-C

Position:

• chr1-173473779-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NR_037845.1(LOC100506023):​n.524+2853C>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 0.0181 in 152,124 control chromosomes in the GnomAD database, including 37 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 0.018 (37 hom., cov: 32)
• Consequence: LOC100506023 NR_037845.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.656

Genes affected

PRDX6-AS1 (HGNC:54870): (PRDX6 antisense RNA 1)

LOC100506023 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BS1: Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.0181 (2754/152124) while in subpopulation SAS AF= 0.0315 (152/4820). AF 95% confidence interval is 0.0274. There are 37 homozygotes in gnomad4. There are 1438 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 37 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC100506023	NR_037845.1	n.524+2853C>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PRDX6-AS1	ENST00000669220.1	n.117+15512C>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0181 AC: 2756 AN: 152006 Hom.: 37 Cov.: 32

Gnomad AFR AF: 0.00358

Gnomad AMI AF: 0.0473

Gnomad AMR AF: 0.0113

Gnomad ASJ AF: 0.0291

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0317

Gnomad FIN AF: 0.0560

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0221

Gnomad OTH AF: 0.0163

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

GnomAD4 genome AF: 0.0181 AC: 2754 AN: 152124 Hom.: 37 Cov.: 32 AF XY: 0.0193 AC XY: 1438 AN XY: 74360

Gnomad4 AFR AF: 0.00357

Gnomad4 AMR AF: 0.0113

Gnomad4 ASJ AF: 0.0291

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.0315

Gnomad4 FIN AF: 0.0560

Gnomad4 NFE AF: 0.0221

Gnomad4 OTH AF: 0.0161

Alfa AF: 0.00765 Hom.: 2

Bravo AF: 0.0140

Asia WGS AF: 0.0140 AC: 48 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.6
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs113102066; hg19: chr1-173442918;