rs879022

chr2-79137337-C-T

Variant summary

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

The ENST00000377435.8(ENSG00000290771):n.167G>A variant causes a splice region, non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0427 in 500,628 control chromosomes in the GnomAD database, including 751 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 0.039 (174 hom., cov: 32)
  • Exomes 𝑓: 0.044 (577 hom.)
• Consequence: ENST00000377435.8 splice_region, non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0690

Genes affected

(HGNC:):

REG1CP (HGNC:9953): (regenerating family member 1 gamma, pseudogene)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0585 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
REG1CP	NR_002714.1	n.1091G>A		non_coding_transcript_exon_variant	1/1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000444841.5	n.172G>A		non_coding_transcript_exon_variant	3/4	1
REG1CP	ENST00000447469.5	n.70G>A		non_coding_transcript_exon_variant	2/5

Frequencies

GnomAD3 genomes AF: 0.0389 AC: 5914 AN: 152100 Hom.: 173 Cov.: 32

Gnomad AFR AF: 0.0113

Gnomad AMI AF: 0.0505

Gnomad AMR AF: 0.0455

Gnomad ASJ AF: 0.0704

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00807

Gnomad FIN AF: 0.0200

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0600

Gnomad OTH AF: 0.0498

GnomAD4 exome AF: 0.0444 AC: 15452 AN: 348410 Hom.: 577 Cov.: 0 AF XY: 0.0431 AC XY: 8581 AN XY: 199106

Gnomad4 AFR exome AF: 0.0137

Gnomad4 AMR exome AF: 0.0307

Gnomad4 ASJ exome AF: 0.0811

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00861

Gnomad4 FIN exome AF: 0.0269

Gnomad4 NFE exome AF: 0.0633

Gnomad4 OTH exome AF: 0.0497

GnomAD4 genome AF: 0.0388 AC: 5908 AN: 152218 Hom.: 174 Cov.: 32 AF XY: 0.0376 AC XY: 2796 AN XY: 74440

Gnomad4 AFR AF: 0.0112

Gnomad4 AMR AF: 0.0455

Gnomad4 ASJ AF: 0.0704

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00787

Gnomad4 FIN AF: 0.0200

Gnomad4 NFE AF: 0.0600

Gnomad4 OTH AF: 0.0492

Alfa AF: 0.0525 Hom.: 79

Bravo AF: 0.0400

Asia WGS AF: 0.00606 AC: 21 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	3.0
Dann	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs879022; hg19: chr2-79364463;