rs35152701

chr1-173475507-G-A

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+1125C>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 0.0212 in 152,290 control chromosomes in the GnomAD database, including 44 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 0.021 (44 hom., cov: 34)
• Consequence: LOC100506023 NR_037845.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.21

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=-0.91).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0212 (3223/152290) while in subpopulation NFE AF= 0.0327 (2225/68006). AF 95% confidence interval is 0.0316. There are 44 homozygotes in gnomad4. There are 1555 alleles in male gnomad4 subpopulation. Median coverage is 34. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 44 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC100506023	NR_037845.1	n.524+1125C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PRDX6-AS1	ENST00000669220.1	n.117+13784C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0212 AC: 3220 AN: 152172 Hom.: 44 Cov.: 34

Gnomad AFR AF: 0.00635

Gnomad AMI AF: 0.0647

Gnomad AMR AF: 0.0185

Gnomad ASJ AF: 0.0176

Gnomad EAS AF: 0.000384

Gnomad SAS AF: 0.0110

Gnomad FIN AF: 0.0228

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.0327

Gnomad OTH AF: 0.0143

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

GnomAD4 genome AF: 0.0212 AC: 3223 AN: 152290 Hom.: 44 Cov.: 34 AF XY: 0.0209 AC XY: 1555 AN XY: 74482

Gnomad4 AFR AF: 0.00633

Gnomad4 AMR AF: 0.0185

Gnomad4 ASJ AF: 0.0176

Gnomad4 EAS AF: 0.000385

Gnomad4 SAS AF: 0.0116

Gnomad4 FIN AF: 0.0228

Gnomad4 NFE AF: 0.0327

Gnomad4 OTH AF: 0.0142

Alfa AF: 0.0282 Hom.: 13

Bravo AF: 0.0190

Asia WGS AF: 0.00577 AC: 20 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.31
Dann	Benign	0.20

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs35152701; hg19: chr1-173444646;