rs1051764

chr7-150373574-T-C

Variant summary

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

The NM_001099695.2(REPIN1):c.*629T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.38 in 168,834 control chromosomes in the GnomAD database, including 12,711 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 0.38 (11245 hom., cov: 33)
  • Exomes 𝑓: 0.41 (1466 hom.)
• Consequence: REPIN1 NM_001099695.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.560

Genes affected

REPIN1 (HGNC:17922): (replication initiator 1) Enables RNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to act upstream of or within positive regulation of glucose import and regulation of fatty acid transport. Located in nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ZNF775 (HGNC:28501): (zinc finger protein 775) Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be active in nucleus. [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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.482 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
REPIN1	NM_001099695.2	c.*629T>C		3_prime_UTR_variant	3/3	ENST00000489432.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
REPIN1	ENST00000489432.7	c.*629T>C		3_prime_UTR_variant	3/3	2	NM_001099695.2	P4

Frequencies

GnomAD3 genomes AF: 0.376 AC: 57122 AN: 151942 Hom.: 11234 Cov.: 33

Gnomad AFR AF: 0.462

Gnomad AMI AF: 0.407

Gnomad AMR AF: 0.254

Gnomad ASJ AF: 0.429

Gnomad EAS AF: 0.497

Gnomad SAS AF: 0.479

Gnomad FIN AF: 0.433

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.323

Gnomad OTH AF: 0.333

GnomAD4 exome AF: 0.412 AC: 6911 AN: 16774 Hom.: 1466 Cov.: 0 AF XY: 0.413 AC XY: 3329 AN XY: 8054

Gnomad4 AFR exome AF: 0.400

Gnomad4 AMR exome AF: 0.220

Gnomad4 ASJ exome AF: 0.500

Gnomad4 EAS exome AF: 0.333

Gnomad4 SAS exome AF: 0.485

Gnomad4 FIN exome AF: 0.428

Gnomad4 NFE exome AF: 0.310

Gnomad4 OTH exome AF: 0.355

GnomAD4 genome AF: 0.376 AC: 57171 AN: 152060 Hom.: 11245 Cov.: 33 AF XY: 0.385 AC XY: 28593 AN XY: 74336

Gnomad4 AFR AF: 0.463

Gnomad4 AMR AF: 0.254

Gnomad4 ASJ AF: 0.429

Gnomad4 EAS AF: 0.498

Gnomad4 SAS AF: 0.478

Gnomad4 FIN AF: 0.433

Gnomad4 NFE AF: 0.323

Gnomad4 OTH AF: 0.333

Alfa AF: 0.348 Hom.: 7266

Bravo AF: 0.364

Asia WGS AF: 0.472 AC: 1642 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	3.0
Dann	Benign	0.49

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: rs1051764; hg19: chr7-150070663; COSMIC: COSV68292348; COSMIC: COSV68292348;