rs4382766

Positions:

• chr1-173475937-C-T

Variant summary

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

The NR_037845.1(LOC100506023):​n.524+695G>A 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 0.606 in 152,174 control chromosomes in the GnomAD database, including 30,067 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 0.61 (30067 hom., cov: 33)
• Consequence: LOC100506023 NR_037845.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.17

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=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.756 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC100506023	NR_037845.1	n.524+695G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PRDX6-AS1	ENST00000669220.1	n.117+13354G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.607 AC: 92259 AN: 152056 Hom.: 30080 Cov.: 33

Gnomad AFR AF: 0.361

Gnomad AMI AF: 0.714

Gnomad AMR AF: 0.716

Gnomad ASJ AF: 0.641

Gnomad EAS AF: 0.402

Gnomad SAS AF: 0.777

Gnomad FIN AF: 0.720

Gnomad MID AF: 0.691

Gnomad NFE AF: 0.713

Gnomad OTH AF: 0.652

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

GnomAD4 genome AF: 0.606 AC: 92250 AN: 152174 Hom.: 30067 Cov.: 33 AF XY: 0.610 AC XY: 45406 AN XY: 74378

Gnomad4 AFR AF: 0.360

Gnomad4 AMR AF: 0.716

Gnomad4 ASJ AF: 0.641

Gnomad4 EAS AF: 0.402

Gnomad4 SAS AF: 0.776

Gnomad4 FIN AF: 0.720

Gnomad4 NFE AF: 0.713

Gnomad4 OTH AF: 0.650

Alfa AF: 0.638 Hom.: 4721

Bravo AF: 0.591

Asia WGS AF: 0.558 AC: 1940 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	8.0
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4382766; hg19: chr1-173445076;