rs1051760

Positions:

• chr7-150373541-A-G

Variant summary

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

The NM_001099695.2(REPIN1):​c.*596A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.396 in 169,878 control chromosomes in the GnomAD database, including 14,127 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 0.39 (12607 hom., cov: 33)
  • Exomes 𝑓: 0.41 (1520 hom.)
• Consequence: REPIN1 NM_001099695.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.300

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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.522 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
REPIN1	NM_001099695.2	c.*596A>G		3_prime_UTR_variant	3/3	ENST00000489432.7	NP_001093165.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
REPIN1	ENST00000489432.7	c.*596A>G		3_prime_UTR_variant	3/3	2	NM_001099695.2	ENSP00000417291	P4

Frequencies

GnomAD3 genomes AF: 0.394 AC: 59906 AN: 151878 Hom.: 12583 Cov.: 33

Gnomad AFR AF: 0.527

Gnomad AMI AF: 0.409

Gnomad AMR AF: 0.260

Gnomad ASJ AF: 0.429

Gnomad EAS AF: 0.497

Gnomad SAS AF: 0.479

Gnomad FIN AF: 0.434

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.323

Gnomad OTH AF: 0.342

GnomAD4 exome AF: 0.406 AC: 7264 AN: 17882 Hom.: 1520 Cov.: 0 AF XY: 0.408 AC XY: 3518 AN XY: 8624

Gnomad4 AFR exome AF: 0.563

Gnomad4 AMR exome AF: 0.233

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.500

Gnomad4 SAS exome AF: 0.496

Gnomad4 FIN exome AF: 0.428

Gnomad4 NFE exome AF: 0.313

Gnomad4 OTH exome AF: 0.377

GnomAD4 genome AF: 0.395 AC: 59972 AN: 151996 Hom.: 12607 Cov.: 33 AF XY: 0.403 AC XY: 29901 AN XY: 74266

Gnomad4 AFR AF: 0.528

Gnomad4 AMR AF: 0.259

Gnomad4 ASJ AF: 0.429

Gnomad4 EAS AF: 0.497

Gnomad4 SAS AF: 0.478

Gnomad4 FIN AF: 0.434

Gnomad4 NFE AF: 0.323

Gnomad4 OTH AF: 0.341

Alfa AF: 0.336 Hom.: 12019

Bravo AF: 0.385

Asia WGS AF: 0.475 AC: 1653 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	8.5
DANN	Benign	0.43
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs1051760; hg19: chr7-150070630; COSMIC: COSV68292347; COSMIC: COSV68292347;