rs879022

Variant names:

• chr2-79137337-C-T
• rs879022
• ENST00000377435.8:n.167G>A

Variant summary

Our verdict is Benign. The variant received -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: ENSG00000290771 ENST00000377435.8 splice_region, non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0690
• Publications: 4 publications found

Genes affected

ENSG00000290771 (HGNC:):

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000377435.8. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	REG1CP	NR_002714.1		n.1091G>A		non_coding_transcript_exon	Exon 1 of 1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000290771	ENST00000377435.8	TSL:1	n.167G>A		splice_region non_coding_transcript_exon	Exon 3 of 4
	ENSG00000290771	ENST00000444841.5	TSL:1	n.172G>A		non_coding_transcript_exon	Exon 3 of 4
	ENSG00000290771	ENST00000414597.6	TSL:2	n.404G>A		splice_region non_coding_transcript_exon	Exon 2 of 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

African (AFR) AF: 0.0137 AC: 131 AN: 9596

American (AMR) AF: 0.0307 AC: 984 AN: 32092

Ashkenazi Jewish (ASJ) AF: 0.0811 AC: 778 AN: 9594

East Asian (EAS) AF: 0.00 AC: 0 AN: 13166

South Asian (SAS) AF: 0.00861 AC: 536 AN: 62226

European-Finnish (FIN) AF: 0.0269 AC: 654 AN: 24304

Middle Eastern (MID) AF: 0.0915 AC: 237 AN: 2590

European-Non Finnish (NFE) AF: 0.0633 AC: 11364 AN: 179388

Other (OTH) AF: 0.0497 AC: 768 AN: 15454

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

African (AFR) AF: 0.0112 AC: 465 AN: 41520

American (AMR) AF: 0.0455 AC: 696 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0704 AC: 244 AN: 3464

East Asian (EAS) AF: 0.00 AC: 0 AN: 5164

South Asian (SAS) AF: 0.00787 AC: 38 AN: 4826

European-Finnish (FIN) AF: 0.0200 AC: 212 AN: 10622

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.0600 AC: 4083 AN: 68014

Other (OTH) AF: 0.0492 AC: 104 AN: 2112

Alfa AF: 0.0446 Hom.: 113

Bravo AF: 0.0400

Asia WGS AF: 0.00606 AC: 21 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.0
DANN	Benign	0.41
PhyloP100		-0.069

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs879022;

hg19: chr2-79364463;