rs4916363

chr1-173472929-G-Achr1-173472929-G-C

Variant summary

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

The NR_037845.1(LOC100506023):n.524+3703C>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 0.599 in 151,946 control chromosomes in the GnomAD database, including 29,649 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 0.60 (29649 hom., cov: 31)
• Consequence: LOC100506023 NR_037845.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.581

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=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.758 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC100506023	NR_037845.1	n.524+3703C>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+16362C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.599 AC: 90982 AN: 151828 Hom.: 29661 Cov.: 31

Gnomad AFR AF: 0.332

Gnomad AMI AF: 0.715

Gnomad AMR AF: 0.714

Gnomad ASJ AF: 0.642

Gnomad EAS AF: 0.406

Gnomad SAS AF: 0.779

Gnomad FIN AF: 0.721

Gnomad MID AF: 0.687

Gnomad NFE AF: 0.714

Gnomad OTH AF: 0.646

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

GnomAD4 genome AF: 0.599 AC: 90973 AN: 151946 Hom.: 29649 Cov.: 31 AF XY: 0.603 AC XY: 44784 AN XY: 74258

Gnomad4 AFR AF: 0.331

Gnomad4 AMR AF: 0.714

Gnomad4 ASJ AF: 0.642

Gnomad4 EAS AF: 0.406

Gnomad4 SAS AF: 0.779

Gnomad4 FIN AF: 0.721

Gnomad4 NFE AF: 0.714

Gnomad4 OTH AF: 0.644

Alfa AF: 0.644 Hom.: 4128

Bravo AF: 0.582

Asia WGS AF: 0.557 AC: 1939 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	0.79
Dann	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4916363; hg19: chr1-173442068;