chr1-119794162-C-T

Position:

• chr1-119794162-C-T

Variant summary

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

The NM_032044.4(REG4):​c.*456G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.545 in 534,118 control chromosomes in the GnomAD database, including 82,448 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 0.58 (26568 hom., cov: 30)
  • Exomes 𝑓: 0.53 (55880 hom.)
• Consequence: REG4 NM_032044.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.443

Genes affected

REG4 (HGNC:22977): (regenerating family member 4) Enables heparin binding activity and mannan binding activity. Predicted to act upstream of or within response to bacterium. Located in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.729 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
REG4	NM_032044.4	c.*456G>A		3_prime_UTR_variant	6/6	ENST00000256585.10	NP_114433.1
REG4	NM_001159352.2	c.*456G>A		3_prime_UTR_variant	7/7		NP_001152824.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
REG4	ENST00000256585	c.*456G>A		3_prime_UTR_variant	6/6	1	NM_032044.4	ENSP00000256585.5
REG4	ENST00000354219	c.*456G>A		3_prime_UTR_variant	7/7	1		ENSP00000346158.1

Frequencies

GnomAD3 genomes AF: 0.579 AC: 87886 AN: 151674 Hom.: 26532 Cov.: 30

Gnomad AFR AF: 0.736

Gnomad AMI AF: 0.467

Gnomad AMR AF: 0.445

Gnomad ASJ AF: 0.581

Gnomad EAS AF: 0.235

Gnomad SAS AF: 0.570

Gnomad FIN AF: 0.477

Gnomad MID AF: 0.623

Gnomad NFE AF: 0.559

Gnomad OTH AF: 0.573

GnomAD3 exomes AF: 0.513 AC: 125090 AN: 243924 Hom.: 34017 AF XY: 0.522 AC XY: 69842 AN XY: 133698

Gnomad AFR exome AF: 0.741

Gnomad AMR exome AF: 0.351

Gnomad ASJ exome AF: 0.567

Gnomad EAS exome AF: 0.232

Gnomad SAS exome AF: 0.588

Gnomad FIN exome AF: 0.483

Gnomad NFE exome AF: 0.559

Gnomad OTH exome AF: 0.540

GnomAD4 exome AF: 0.531 AC: 202962 AN: 382326 Hom.: 55880 Cov.: 0 AF XY: 0.539 AC XY: 117300 AN XY: 217722

Gnomad4 AFR exome AF: 0.742

Gnomad4 AMR exome AF: 0.353

Gnomad4 ASJ exome AF: 0.569

Gnomad4 EAS exome AF: 0.230

Gnomad4 SAS exome AF: 0.584

Gnomad4 FIN exome AF: 0.484

Gnomad4 NFE exome AF: 0.557

Gnomad4 OTH exome AF: 0.550

GnomAD4 genome AF: 0.580 AC: 87973 AN: 151792 Hom.: 26568 Cov.: 30 AF XY: 0.570 AC XY: 42288 AN XY: 74166

Gnomad4 AFR AF: 0.736

Gnomad4 AMR AF: 0.445

Gnomad4 ASJ AF: 0.581

Gnomad4 EAS AF: 0.235

Gnomad4 SAS AF: 0.569

Gnomad4 FIN AF: 0.477

Gnomad4 NFE AF: 0.559

Gnomad4 OTH AF: 0.575

Alfa AF: 0.562 Hom.: 56641

Bravo AF: 0.580

Asia WGS AF: 0.502 AC: 1748 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	2.3
DANN	Benign	0.59

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs1052972; hg19: chr1-120336785; COSMIC: COSV56652266; COSMIC: COSV56652266;