rs12739142

Positions:

• chr1-173475516-A-G

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+1116T>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 0.0286 in 152,370 control chromosomes in the GnomAD database, including 95 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 0.029 (95 hom., cov: 34)
• Consequence: LOC100506023 NR_037845.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.03

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=-0.9).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0286 (4363/152370) while in subpopulation NFE AF= 0.0452 (3078/68032). AF 95% confidence interval is 0.0439. There are 95 homozygotes in gnomad4. There are 2007 alleles in male gnomad4 subpopulation. Median coverage is 34. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 95 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC100506023	NR_037845.1	n.524+1116T>C		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+13775T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0287 AC: 4367 AN: 152252 Hom.: 95 Cov.: 34

Gnomad AFR AF: 0.00731

Gnomad AMI AF: 0.0779

Gnomad AMR AF: 0.0272

Gnomad ASJ AF: 0.0334

Gnomad EAS AF: 0.000961

Gnomad SAS AF: 0.0120

Gnomad FIN AF: 0.0210

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0452

Gnomad OTH AF: 0.0358

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

GnomAD4 genome AF: 0.0286 AC: 4363 AN: 152370 Hom.: 95 Cov.: 34 AF XY: 0.0269 AC XY: 2007 AN XY: 74510

Gnomad4 AFR AF: 0.00726

Gnomad4 AMR AF: 0.0271

Gnomad4 ASJ AF: 0.0334

Gnomad4 EAS AF: 0.000963

Gnomad4 SAS AF: 0.0120

Gnomad4 FIN AF: 0.0210

Gnomad4 NFE AF: 0.0452

Gnomad4 OTH AF: 0.0350

Alfa AF: 0.0411 Hom.: 29

Bravo AF: 0.0280

Asia WGS AF: 0.00751 AC: 26 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.4
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12739142; hg19: chr1-173444655;